From owner-chemistry@ccl.net Wed Apr 2 01:17:00 2008 From: "Matt James Ketterer mkettere-*-iupui.edu" To: CCL Subject: CCL: Solved--Modification of xyz files to include metals Message-Id: <-36610-080402010949-14076-rFdwrv37CCmUMecNbYd9AQ^server.ccl.net> X-Original-From: "Matt James Ketterer" Date: Wed, 2 Apr 2008 01:09:45 -0400 Sent to CCL by: "Matt James Ketterer" [mkettere a iupui.edu] Hello all. Thanks for the suggestions to my problem. I just want to post the solution that I found with some help from Jay Ponder on editing xyz files to include atoms not read by the pdb converter. Using the xyzedit program, it is easy to change the numbers to put the atom you're adding first before the main chain (I found this was necessary for it to be read). Otherwise you have to manually change all the numbers. So to change all the numbers and put a new atom in the number 1 spot, just type 1,1, and 0 for the three interactive questions it asks in the commmand line executable. Then edit the new xyz file and once you copy the coordinates from the pdb file, put the atom number from the parameter set (amber99 and charm27 contain the metal ions and zinc as well as the protein parameters) right after the coordinates and it should work fine, even if you don't replace the "NEW" for atom type as the parameter will do that with the number as it does the calculation. Thanks again Matt From owner-chemistry@ccl.net Wed Apr 2 03:38:00 2008 From: "Van Dam, HJJ \(Huub\) h.j.j.vandam_+_dl.ac.uk" To: CCL Subject: CCL: Gamess linking problem Message-Id: <-36611-080401122916-32060-6H8L5eEAL3mq4Z4vtBwC3Q(0)server.ccl.net> X-Original-From: "Van Dam, HJJ \(Huub\)" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C89405.796B6F84" Date: Tue, 1 Apr 2008 15:34:20 +0100 MIME-Version: 1.0 Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam]~[dl.ac.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01C89405.796B6F84 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Jones, =20 Just a silly question in response to your request... =20 As far as I know MKL is an Intel math library for fast BLAS operations and such like. Usually I would use that library with the Intel fortran compilers. So why are you trying to compile the code with the GNU gfortran compiler and linking against the Intel MKL library? It seems to me that this combination is likely to cause problems due to missing Intel runtime libraries that the gfortran compiler does not know about. =20 Best wishes, =20 Huub =20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D Huub van Dam (h.j.j.vandam]*[stfc.ac.uk, +44-1925-603933) =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D =20 ________________________________ > From: owner-chemistry]*[ccl.net [mailto:owner-chemistry]*[ccl.net]=20 Sent: 01 April 2008 04:56 To: Vandam, Huub Subject: CCL: Gamess linking problem Hi all. I'm having a stupid problem in compiling gamess. Hope someone here can help me. We are using gfortran together with mkl library. basically, the first option when considering linux64 and intel machines. We are having problems in the linking stage, lked script. I get the following error messages: gfortran -o ../gamess.01.x gamess.o unport.o zunix.o aldeci.o algnci.o basccn.o basecp.o basext.o bashuz.o bashz2.o basn21.o basn31.o baspcn.o bassto.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o cee is.o chgpen.o cisgrd.o cosmo.o cphf.o cpmchf.o cprohf.o ddilib.o delocl.o demrpt.o dft.o dftaux.o dftexc.o dftfun.o dftgrd.o dftint.o dgeev.o dgesvd.o dmulti.o drc.o ecp.o ecpder.o ecplib.o ecppot. o efchtr.o efdrvr.o efgrda.o efgrdb.o efgrdc.o efgrd2.o efinp.o efinta.o efintb.o efelec.o efpaul.o efpcm.o efpcov.o efpfmo.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o ffield.o fmo.o fmoes d.o fmogrd.o fmoint.o fmoio.o fmolib.o fmopbc.o fmoprp.o frfmt.o fsodci.o globop.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss2a.o hss2b.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o int2t.o int2u.o int2v.o int2w.o int2x.o iolib.o ivocas.o la gran.o local.o loccd.o locpol.o mcpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mm23.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcgrd.o mpcint.o mpcmol.o mpcmsc.o morokm.o mthlib.o nameio.o nmr.o ordint.o ormas1.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o p cmdis.o pcmief.o pcmpol.o pcmvch.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o qrel.o raman.o rhfuhf.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o sobrt.o soffac.o solib.o sozeff.o stat pt.o surf.o svpchg.o svpinp.o svpleb.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o umpdd i.o vibanl.o vscf.o vvos.o zapddi.o zheev.o zmatrx.o qmmm.o vbdum.o neostb.o ../ddi/libddi.a -lpthread -L/home/johannes/lib/mkl/lib/em64t -lmkl_em64t -lmkl_lapack -lmkl /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dgemm_omp.o): In function `mkl_blas_dgemm': __tmp_dgemm_omp.c:(.text+0x6c): undefined reference to `__kmpc_global_thread_num' __tmp_dgemm_omp.c:(.text+0x32c): undefined reference to `__kmpc_ok_to_fork' __tmp_dgemm_omp.c:(.text+0x351): undefined reference to `__kmpc_push_num_threads' __tmp_dgemm_omp.c:(.text+0x3c3): undefined reference to `__kmpc_fork_call' __tmp_dgemm_omp.c:(.text+0x3dd): undefined reference to `__kmpc_serialized_parallel' __tmp_dgemm_omp.c:(.text+0x44f): undefined reference to `__kmpc_end_serialized_parallel' __tmp_dgemm_omp.c:(.text+0x53d): undefined reference to `__kmpc_ok_to_fork' __tmp_dgemm_omp.c:(.text+0x562): undefined reference to `__kmpc_push_num_threads' __tmp_dgemm_omp.c:(.text+0x656): undefined reference to `__kmpc_fork_call' __tmp_dgemm_omp.c:(.text+0x670): undefined reference to `__kmpc_serialized_parallel' __tmp_dgemm_omp.c:(.text+0x743): undefined reference to `__kmpc_end_serialized_parallel' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dgemm_omp.o): In function `L_mkl_blas_dgemm_570__par_loop2': __tmp_dgemm_omp.c:(.text+0xaec): undefined reference to `__kmpc_for_static_init_8' __tmp_dgemm_omp.c:(.text+0xd72): undefined reference to `__kmpc_for_static_fini' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dgemm_omp.o): In function `L_mkl_blas_dgemm_557__par_loop1': __tmp_dgemm_omp.c:(.text+0xf3d): undefined reference to `__kmpc_for_static_init_8' __tmp_dgemm_omp.c:(.text+0x10ec): undefined reference to `__kmpc_for_static_fini' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dgemm_omp.o): In function `L_mkl_blas_dgemm_601__par_loop3': __tmp_dgemm_omp.c:(.text+0x12f3): undefined reference to `__kmpc_for_static_init_8' __tmp_dgemm_omp.c:(.text+0x152a): undefined reference to `__kmpc_for_static_fini' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dgemm_omp.o): In function `L_mkl_blas_dgemm_467__par_loop0': __tmp_dgemm_omp.c:(.text+0x166b): undefined reference to `__kmpc_for_static_init_8' __tmp_dgemm_omp.c:(.text+0x1776): undefined reference to `__kmpc_for_static_fini' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dgemm_omp.o): In function `dgemm_1D': __tmp_dgemm_omp.c:(.text+0x1931): undefined reference to `__kmpc_global_thread_num' __tmp_dgemm_omp.c:(.text+0x19ed): undefined reference to `__kmpc_ok_to_fork' __tmp_dgemm_omp.c:(.text+0x1a12): undefined reference to `__kmpc_push_num_threads' __tmp_dgemm_omp.c:(.text+0x1aca): undefined reference to `__kmpc_fork_call' __tmp_dgemm_omp.c:(.text+0x1ae8): undefined reference to `__kmpc_serialized_parallel' __tmp_dgemm_omp.c:(.text+0x1bd9): undefined reference to `__kmpc_end_serialized_parallel' __tmp_dgemm_omp.c:(.text+0x1c2d): undefined reference to `__kmpc_ok_to_fork' __tmp_dgemm_omp.c:(.text+0x1c52): undefined reference to `__kmpc_push_num_threads' __tmp_dgemm_omp.c:(.text+0x1d46): undefined reference to `__kmpc_fork_call' __tmp_dgemm_omp.c:(.text+0x1d60): undefined reference to `__kmpc_serialized_parallel' __tmp_dgemm_omp.c:(.text+0x1e33): undefined reference to `__kmpc_end_serialized_parallel' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dgemm_omp.o): In function `L_dgemm_1D_665__par_loop4': __tmp_dgemm_omp.c:(.text+0x2022): undefined reference to `__kmpc_for_static_init_8' __tmp_dgemm_omp.c:(.text+0x21c8): undefined reference to `__kmpc_for_static_fini' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dgemm_omp.o): In function `L_dgemm_1D_678__par_loop5': __tmp_dgemm_omp.c:(.text+0x23c9): undefined reference to `__kmpc_for_static_init_8' __tmp_dgemm_omp.c:(.text+0x257a): undefined reference to `__kmpc_for_static_fini' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dtrmm_omp.o): In function `mkl_blas_dtrmm': __tmp_dtrmm_omp.c:(.text+0x68): undefined reference to `__kmpc_global_thread_num' __tmp_dtrmm_omp.c:(.text+0x1a4): undefined reference to `__kmpc_ok_to_fork' __tmp_dtrmm_omp.c:(.text+0x1c9): undefined reference to `__kmpc_push_num_threads' __tmp_dtrmm_omp.c:(.text+0x280): undefined reference to `__kmpc_fork_call' __tmp_dtrmm_omp.c:(.text+0x29a): undefined reference to `__kmpc_serialized_parallel' __tmp_dtrmm_omp.c:(.text+0x33f): undefined reference to `__kmpc_end_serialized_parallel' __tmp_dtrmm_omp.c:(.text+0x352): undefined reference to `__kmpc_ok_to_fork' __tmp_dtrmm_omp.c:(.text+0x377): undefined reference to `__kmpc_push_num_threads' __tmp_dtrmm_omp.c:(.text+0x400): undefined reference to `__kmpc_fork_call' __tmp_dtrmm_omp.c:(.text+0x41e): undefined reference to `__kmpc_serialized_parallel' __tmp_dtrmm_omp.c:(.text+0x4d2): undefined reference to `__kmpc_end_serialized_parallel' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dtrmm_omp.o): In function `L_mkl_blas_dtrmm_236__par_loop0': __tmp_dtrmm_omp.c:(.text+0x730): undefined reference to `__kmpc_for_static_init_8' __tmp_dtrmm_omp.c:(.text+0x897): undefined reference to `__kmpc_for_static_fini' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dtrmm_omp.o): In function `L_mkl_blas_dtrmm_256__par_loop1': __tmp_dtrmm_omp.c:(.text+0xa36): undefined reference to `__kmpc_for_static_init_8' __tmp_dtrmm_omp.c:(.text+0xb97): undefined reference to `__kmpc_for_static_fini' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dtrsm_omp.o): In function `mkl_blas_dtrsm': __tmp_dtrsm_omp.c:(.text+0x68): undefined reference to `__kmpc_global_thread_num' __tmp_dtrsm_omp.c:(.text+0x1a2): undefined reference to `__kmpc_ok_to_fork' __tmp_dtrsm_omp.c:(.text+0x1c7): undefined reference to `__kmpc_push_num_threads' __tmp_dtrsm_omp.c:(.text+0x27b): undefined reference to `__kmpc_fork_call' __tmp_dtrsm_omp.c:(.text+0x295): undefined reference to `__kmpc_serialized_parallel' __tmp_dtrsm_omp.c:(.text+0x337): undefined reference to `__kmpc_end_serialized_parallel' __tmp_dtrsm_omp.c:(.text+0x34a): undefined reference to `__kmpc_ok_to_fork' __tmp_dtrsm_omp.c:(.text+0x36f): undefined reference to `__kmpc_push_num_threads' __tmp_dtrsm_omp.c:(.text+0x3f5): undefined reference to `__kmpc_fork_call' __tmp_dtrsm_omp.c:(.text+0x413): undefined reference to `__kmpc_serialized_parallel' __tmp_dtrsm_omp.c:(.text+0x4c4): undefined reference to `__kmpc_end_serialized_parallel' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dtrsm_omp.o): In function `L_mkl_blas_dtrsm_259__par_loop0': __tmp_dtrsm_omp.c:(.text+0x722): undefined reference to `__kmpc_for_static_init_8' __tmp_dtrsm_omp.c:(.text+0x88f): undefined reference to `__kmpc_for_static_fini' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dtrsm_omp.o): In function `L_mkl_blas_dtrsm_276__par_loop1': __tmp_dtrsm_omp.c:(.text+0xa2e): undefined reference to `__kmpc_for_static_init_8' __tmp_dtrsm_omp.c:(.text+0xb8f): undefined reference to `__kmpc_for_static_fini' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(mkl_threading.o): In function `MKL_Get_Max_Threads': __tmp_mkl_threading.c:(.text+0x55): undefined reference to `omp_in_parallel' __tmp_mkl_threading.c:(.text+0x77): undefined reference to `omp_get_max_threads' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(mkl_threading.o): In function `MKL_Domain_Get_Max_Threads': __tmp_mkl_threading.c:(.text+0x855): undefined reference to `omp_in_parallel' __tmp_mkl_threading.c:(.text+0x874): undefined reference to `omp_get_max_threads' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `__kmpc_ordered' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `omp_get_thread_num' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `__kmpc_barrier' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `omp_get_num_procs' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `__kmpc_critical' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_8' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `__kmpc_end_critical' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_8' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_4' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `__kmpc_flush' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_8' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `__kmpc_end_ordered' /home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed8_add' collect2: ld returned 1 exit status unset echo I'm using the last stable versions of both mkl and gamess. Does anybody has any clue on this? Have anybody please gone throw such a problem? Thanks a lot to everybody in advance. Sincerally yours, Jones ------_=_NextPart_001_01C89405.796B6F84 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Hi Jones,
 
Just a silly question in response to your=20 request...
 
As far as I know MKL is an Intel math library = for fast BLAS=20 operations and such like. Usually I would use that library with the = Intel=20 fortran compilers. So why are you trying to compile the code with the = GNU=20 gfortran compiler and linking against the Intel MKL library? It seems to = me that=20 this combination is likely to cause problems due to missing Intel = runtime=20 libraries that the gfortran compiler does not know = about.
 
Best wishes,
 
   Huub
 

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Huub van=20 Dam (h.j.j.vandam]*[stfc.ac.uk,=20 +44-1925-603933)
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

 

From: owner-chemistry]*[ccl.net=20 [mailto:owner-chemistry]*[ccl.net]
Sent: 01 April 2008=20 04:56
To: Vandam, Huub
Subject: CCL: Gamess = linking=20 problem

Hi all.

I'm having a stupid problem in compiling = gamess. Hope=20 someone here can help me.

We are using gfortran together with mkl = library. basically, the first option when considering linux64 and intel=20 machines.

We are having problems in the linking stage, lked = script. I get=20 the following error messages:


gfortran -o ../gamess.01.x = gamess.o=20 unport.o zunix.o aldeci.o algnci.o basccn.o basecp.o basext.o bashuz.o = bashz2.o=20 basn21.o basn31.o baspcn.o bassto.o ccaux.o ccddi.o ccqaux.o ccquad.o = ccsdt.o=20 cee
is.o chgpen.o cisgrd.o cosmo.o cphf.o cpmchf.o cprohf.o ddilib.o = delocl.o=20 demrpt.o dft.o dftaux.o dftexc.o dftfun.o dftgrd.o dftint.o dgeev.o = dgesvd.o=20 dmulti.o drc.o ecp.o ecpder.o ecplib.o ecppot.
o efchtr.o efdrvr.o = efgrda.o=20 efgrdb.o efgrdc.o efgrd2.o efinp.o efinta.o efintb.o efelec.o efpaul.o = efpcm.o=20 efpcov.o efpfmo.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o = ffield.o=20 fmo.o fmoes
d.o fmogrd.o fmoint.o fmoio.o fmolib.o fmopbc.o fmoprp.o = frfmt.o=20 fsodci.o globop.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o = gugdga.o=20 gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o = gvb.o
 hess.o=20 hss1a.o hss1b.o hss2a.o hss2b.o inputa.o inputb.o inputc.o int1.o = int2a.o=20 int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o int2t.o int2u.o = int2v.o=20 int2w.o int2x.o iolib.o ivocas.o la
gran.o local.o loccd.o locpol.o = mcpgrd.o=20 mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o = mcpl70.o=20 mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o=20 mdefp.o
mexing.o mm23.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o = mpcdat.o=20 mpcgrd.o mpcint.o mpcmol.o mpcmsc.o morokm.o mthlib.o nameio.o nmr.o = ordint.o=20 ormas1.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o p
cmdis.o pcmief.o = pcmpol.o pcmvch.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o = qrel.o=20 raman.o rhfuhf.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o = sobrt.o=20 soffac.o solib.o sozeff.o stat
pt.o surf.o svpchg.o svpinp.o svpleb.o = symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o = tdhf.o=20 tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o = trudge.o=20 umpdd
i.o vibanl.o vscf.o vvos.o zapddi.o zheev.o zmatrx.o qmmm.o = vbdum.o=20 neostb.o ../ddi/libddi.a -lpthread -L/home/johannes/lib/mkl/lib/em64t=20 -lmkl_em64t -lmkl_lapack=20 -lmkl
/home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.a(dgemm_omp= .o): In=20 function `mkl_blas_dgemm':
__tmp_dgemm_omp.c:(.text+0x6c): undefined=20 reference to = `__kmpc_global_thread_num'
__tmp_dgemm_omp.c:(.text+0x32c):=20 undefined reference to = `__kmpc_ok_to_fork'
__tmp_dgemm_omp.c:(.text+0x351):=20 undefined reference to=20 `__kmpc_push_num_threads'
__tmp_dgemm_omp.c:(.text+0x3c3): undefined=20 reference to `__kmpc_fork_call'
__tmp_dgemm_omp.c:(.text+0x3dd): = undefined=20 reference to = `__kmpc_serialized_parallel'
__tmp_dgemm_omp.c:(.text+0x44f):=20 undefined reference to=20 `__kmpc_end_serialized_parallel'
__tmp_dgemm_omp.c:(.text+0x53d): = undefined=20 reference to `__kmpc_ok_to_fork'
__tmp_dgemm_omp.c:(.text+0x562): = undefined=20 reference to = `__kmpc_push_num_threads'
__tmp_dgemm_omp.c:(.text+0x656):=20 undefined reference to = `__kmpc_fork_call'
__tmp_dgemm_omp.c:(.text+0x670):=20 undefined reference to=20 `__kmpc_serialized_parallel'
__tmp_dgemm_omp.c:(.text+0x743): = undefined=20 reference to=20 `__kmpc_end_serialized_parallel'
/home/johannes/lib/mkl/lib/em64t/libm= kl_intel_thread.a(dgemm_omp.o):=20 In function=20 `L_mkl_blas_dgemm_570__par_loop2':
__tmp_dgemm_omp.c:(.text+0xaec): = undefined=20 reference to = `__kmpc_for_static_init_8'
__tmp_dgemm_omp.c:(.text+0xd72):=20 undefined reference to=20 `__kmpc_for_static_fini'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.a(dgemm_omp.o):=20 In function=20 `L_mkl_blas_dgemm_557__par_loop1':
__tmp_dgemm_omp.c:(.text+0xf3d): = undefined=20 reference to = `__kmpc_for_static_init_8'
__tmp_dgemm_omp.c:(.text+0x10ec):=20 undefined reference to=20 `__kmpc_for_static_fini'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.a(dgemm_omp.o):=20 In function=20 `L_mkl_blas_dgemm_601__par_loop3':
__tmp_dgemm_omp.c:(.text+0x12f3):=20 undefined reference to=20 `__kmpc_for_static_init_8'
__tmp_dgemm_omp.c:(.text+0x152a): = undefined=20 reference to=20 `__kmpc_for_static_fini'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.a(dgemm_omp.o):=20 In function=20 `L_mkl_blas_dgemm_467__par_loop0':
__tmp_dgemm_omp.c:(.text+0x166b):=20 undefined reference to=20 `__kmpc_for_static_init_8'
__tmp_dgemm_omp.c:(.text+0x1776): = undefined=20 reference to=20 `__kmpc_for_static_fini'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.a(dgemm_omp.o):=20 In function `dgemm_1D':
__tmp_dgemm_omp.c:(.text+0x1931): undefined = reference=20 to `__kmpc_global_thread_num'
__tmp_dgemm_omp.c:(.text+0x19ed): = undefined=20 reference to `__kmpc_ok_to_fork'
__tmp_dgemm_omp.c:(.text+0x1a12): = undefined=20 reference to = `__kmpc_push_num_threads'
__tmp_dgemm_omp.c:(.text+0x1aca):=20 undefined reference to = `__kmpc_fork_call'
__tmp_dgemm_omp.c:(.text+0x1ae8):=20 undefined reference to=20 `__kmpc_serialized_parallel'
__tmp_dgemm_omp.c:(.text+0x1bd9): = undefined=20 reference to=20 `__kmpc_end_serialized_parallel'
__tmp_dgemm_omp.c:(.text+0x1c2d): = undefined=20 reference to `__kmpc_ok_to_fork'
__tmp_dgemm_omp.c:(.text+0x1c52): = undefined=20 reference to = `__kmpc_push_num_threads'
__tmp_dgemm_omp.c:(.text+0x1d46):=20 undefined reference to = `__kmpc_fork_call'
__tmp_dgemm_omp.c:(.text+0x1d60):=20 undefined reference to=20 `__kmpc_serialized_parallel'
__tmp_dgemm_omp.c:(.text+0x1e33): = undefined=20 reference to=20 `__kmpc_end_serialized_parallel'
/home/johannes/lib/mkl/lib/em64t/libm= kl_intel_thread.a(dgemm_omp.o):=20 In function = `L_dgemm_1D_665__par_loop4':
__tmp_dgemm_omp.c:(.text+0x2022):=20 undefined reference to=20 `__kmpc_for_static_init_8'
__tmp_dgemm_omp.c:(.text+0x21c8): = undefined=20 reference to=20 `__kmpc_for_static_fini'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.a(dgemm_omp.o):=20 In function = `L_dgemm_1D_678__par_loop5':
__tmp_dgemm_omp.c:(.text+0x23c9):=20 undefined reference to=20 `__kmpc_for_static_init_8'
__tmp_dgemm_omp.c:(.text+0x257a): = undefined=20 reference to=20 `__kmpc_for_static_fini'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.a(dtrmm_omp.o):=20 In function `mkl_blas_dtrmm':
__tmp_dtrmm_omp.c:(.text+0x68): = undefined=20 reference to = `__kmpc_global_thread_num'
__tmp_dtrmm_omp.c:(.text+0x1a4):=20 undefined reference to = `__kmpc_ok_to_fork'
__tmp_dtrmm_omp.c:(.text+0x1c9):=20 undefined reference to=20 `__kmpc_push_num_threads'
__tmp_dtrmm_omp.c:(.text+0x280): undefined=20 reference to `__kmpc_fork_call'
__tmp_dtrmm_omp.c:(.text+0x29a): = undefined=20 reference to = `__kmpc_serialized_parallel'
__tmp_dtrmm_omp.c:(.text+0x33f):=20 undefined reference to=20 `__kmpc_end_serialized_parallel'
__tmp_dtrmm_omp.c:(.text+0x352): = undefined=20 reference to `__kmpc_ok_to_fork'
__tmp_dtrmm_omp.c:(.text+0x377): = undefined=20 reference to = `__kmpc_push_num_threads'
__tmp_dtrmm_omp.c:(.text+0x400):=20 undefined reference to = `__kmpc_fork_call'
__tmp_dtrmm_omp.c:(.text+0x41e):=20 undefined reference to=20 `__kmpc_serialized_parallel'
__tmp_dtrmm_omp.c:(.text+0x4d2): = undefined=20 reference to=20 `__kmpc_end_serialized_parallel'
/home/johannes/lib/mkl/lib/em64t/libm= kl_intel_thread.a(dtrmm_omp.o):=20 In function=20 `L_mkl_blas_dtrmm_236__par_loop0':
__tmp_dtrmm_omp.c:(.text+0x730): = undefined=20 reference to = `__kmpc_for_static_init_8'
__tmp_dtrmm_omp.c:(.text+0x897):=20 undefined reference to=20 `__kmpc_for_static_fini'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.a(dtrmm_omp.o):=20 In function=20 `L_mkl_blas_dtrmm_256__par_loop1':
__tmp_dtrmm_omp.c:(.text+0xa36): = undefined=20 reference to = `__kmpc_for_static_init_8'
__tmp_dtrmm_omp.c:(.text+0xb97):=20 undefined reference to=20 `__kmpc_for_static_fini'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.a(dtrsm_omp.o):=20 In function `mkl_blas_dtrsm':
__tmp_dtrsm_omp.c:(.text+0x68): = undefined=20 reference to = `__kmpc_global_thread_num'
__tmp_dtrsm_omp.c:(.text+0x1a2):=20 undefined reference to = `__kmpc_ok_to_fork'
__tmp_dtrsm_omp.c:(.text+0x1c7):=20 undefined reference to=20 `__kmpc_push_num_threads'
__tmp_dtrsm_omp.c:(.text+0x27b): undefined=20 reference to `__kmpc_fork_call'
__tmp_dtrsm_omp.c:(.text+0x295): = undefined=20 reference to = `__kmpc_serialized_parallel'
__tmp_dtrsm_omp.c:(.text+0x337):=20 undefined reference to=20 `__kmpc_end_serialized_parallel'
__tmp_dtrsm_omp.c:(.text+0x34a): = undefined=20 reference to `__kmpc_ok_to_fork'
__tmp_dtrsm_omp.c:(.text+0x36f): = undefined=20 reference to = `__kmpc_push_num_threads'
__tmp_dtrsm_omp.c:(.text+0x3f5):=20 undefined reference to = `__kmpc_fork_call'
__tmp_dtrsm_omp.c:(.text+0x413):=20 undefined reference to=20 `__kmpc_serialized_parallel'
__tmp_dtrsm_omp.c:(.text+0x4c4): = undefined=20 reference to=20 `__kmpc_end_serialized_parallel'
/home/johannes/lib/mkl/lib/em64t/libm= kl_intel_thread.a(dtrsm_omp.o):=20 In function=20 `L_mkl_blas_dtrsm_259__par_loop0':
__tmp_dtrsm_omp.c:(.text+0x722): = undefined=20 reference to = `__kmpc_for_static_init_8'
__tmp_dtrsm_omp.c:(.text+0x88f):=20 undefined reference to=20 `__kmpc_for_static_fini'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.a(dtrsm_omp.o):=20 In function=20 `L_mkl_blas_dtrsm_276__par_loop1':
__tmp_dtrsm_omp.c:(.text+0xa2e): = undefined=20 reference to = `__kmpc_for_static_init_8'
__tmp_dtrsm_omp.c:(.text+0xb8f):=20 undefined reference to=20 `__kmpc_for_static_fini'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.a(mkl_threading.o):=20 In function = `MKL_Get_Max_Threads':
__tmp_mkl_threading.c:(.text+0x55):=20 undefined reference to = `omp_in_parallel'
__tmp_mkl_threading.c:(.text+0x77):=20 undefined reference to=20 `omp_get_max_threads'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel_th= read.a(mkl_threading.o):=20 In function=20 `MKL_Domain_Get_Max_Threads':
__tmp_mkl_threading.c:(.text+0x855): = undefined=20 reference to `omp_in_parallel'
__tmp_mkl_threading.c:(.text+0x874): = undefined=20 reference to=20 `omp_get_max_threads'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel_th= read.so:=20 undefined reference to=20 `__kmpc_ordered'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.= so:=20 undefined reference to=20 `omp_get_thread_num'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel_thr= ead.so:=20 undefined reference to=20 `__kmpc_barrier'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.= so:=20 undefined reference to=20 `omp_get_num_procs'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel_thre= ad.so:=20 undefined reference to=20 `__kmpc_critical'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread= .so:=20 undefined reference to=20 `__kmpc_dispatch_fini_8'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.so:=20 undefined reference to=20 `__kmpc_end_critical'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel_th= read.so:=20 undefined reference to=20 `__kmpc_dispatch_init_8'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.so:=20 undefined reference to=20 `__kmpc_for_static_init_4'
/home/johannes/lib/mkl/lib/em64t/libmkl_int= el_thread.so:=20 undefined reference to=20 `__kmpc_flush'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel_thread.so= :=20 undefined reference to=20 `__kmpc_dispatch_next_8'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel= _thread.so:=20 undefined reference to=20 `__kmpc_end_ordered'
/home/johannes/lib/mkl/lib/em64t/libmkl_intel_thr= ead.so:=20 undefined reference to `__kmpc_atomic_fixed8_add'
collect2: ld = returned 1=20 exit status
unset echo


I'm using the last stable versions = of both=20 mkl and gamess. Does anybody has any clue on this? Have anybody please = gone=20 throw such a problem?

Thanks a lot to everybody in=20 advance.

Sincerally yours,

Jones
------_=_NextPart_001_01C89405.796B6F84-- From owner-chemistry@ccl.net Wed Apr 2 04:57:00 2008 From: "Justin Finnerty justin.finnerty+/-uni-oldenburg.de" To: CCL Subject: CCL: Gamess linking problem Message-Id: <-36612-080402045259-12366-CGPFO8wZmGzeJLkDWbCDdg!=!server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 02 Apr 2008 10:52:39 +0200 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty__uni-oldenburg.de] Hello, I think that the GNU compilers should be able to link with MKL. However the error messages seem to be complaining about OpenMP functions. Recently the GNU compilers (>4.2) have added support for OpenMP. This may require you to change the command line with additional options -fopenmp and linker with -lgomp. The introduction of OpenMP (among other things) has changed the options and libraries necessary when using the current GNU compilers. This has made many packages out-of-date with-respect-to using GNU compilers and will require manual changes to makefiles until software providers catch up. Cheers Justin > -- Dr Justin Finnerty Rm W3-1-165 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Wed Apr 2 08:19:00 2008 From: "Syed Tarique Moin tarisyed_._yahoo.com" To: CCL Subject: CCL: quadratic force constants from hessians Message-Id: <-36613-080402081359-9689-s21tyVqudIc83JyR6RYmCA_+_server.ccl.net> X-Original-From: "Syed Tarique Moin" Date: Wed, 2 Apr 2008 08:13:55 -0400 Sent to CCL by: "Syed Tarique Moin" [tarisyed^_^yahoo.com] Dear all, I carried out single point calculation for a complex but i want to get force constants for the bond length and bond angle. Can anyone guide me how to do this. Regards From owner-chemistry@ccl.net Wed Apr 2 09:07:01 2008 From: "jamel-eddine.meslamani*_*ulp.u-strasbg.fr" To: CCL Subject: CCL: MOL2 program viewer Message-Id: <-36614-080402062809-31474-4s151BQXxUrvrjgJG9iAzw[a]server.ccl.net> X-Original-From: jamel-eddine.meslamani-#-ulp.u-strasbg.fr Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 02 Apr 2008 11:48:42 +0200 MIME-Version: 1.0 Sent to CCL by: jamel-eddine.meslamani[A]ulp.u-strasbg.fr Dear cclrs, Actually I'd like to know if there is an open source program that could display molecules in mol2 format and to color all of them in a one step. I'm using linux as OS. Thank you in advance for answers. Meslamani Jamel From owner-chemistry@ccl.net Wed Apr 2 11:18:00 2008 From: "Adlane sayede adlane.sayede .. gmail.com" To: CCL Subject: CCL: MOL2 program viewer Message-Id: <-36615-080402111602-18772-eqbexNY9/giggKLUfHlBDg##server.ccl.net> X-Original-From: "Adlane sayede" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 2 Apr 2008 15:38:02 +0200 MIME-Version: 1.0 Sent to CCL by: "Adlane sayede" [adlane.sayede{}gmail.com] Hi, try molden which is free and nice http://www.cmbi.ru.nl/molden/molden.html Adlane Sayede --=20 Sayede Adlane Ma=EEtre de Conf=E9rences en Chimie UCCS - UMR CNRS 8181, F=E9d=E9ration Chevreul - FR CNRS 2638 Universit=E9 d'Artois Facult=E9 des Sciences Jean Perrin Rue Jean Souvraz SP 18 62307 LENS FRANCE e-mail: adlane.sayede.:..univ-artois.fr http://www.lpcia.univ-artois.fr/adlanesayede.htm Phone: +33 321 791 771 Fax: +33 321 791 755 On Wed, Apr 2, 2008 at 11:48 AM, jamel-eddine.meslamani*_*ulp.u-strasbg.fr wrote: > > Sent to CCL by: jamel-eddine.meslamani[A]ulp.u-strasbg.fr > Dear cclrs, > > Actually I'd like to know if there is an open source program that could d= isplay molecules in mol2 format and to color all of them in a one step. > I'm using linux as OS. > Thank you in advance for answers. > > Meslamani Jamel > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: http://server.ccl.net/chemistry/= announcements/conferences/> > > From owner-chemistry@ccl.net Wed Apr 2 11:53:00 2008 From: "Marius Retegan marius.s.retegan++gmail.com" To: CCL Subject: CCL: MOL2 program viewer Message-Id: <-36616-080402111541-18712-emnUJGym9/gfN1qaqCvh4w]|[server.ccl.net> X-Original-From: "Marius Retegan" Content-Type: multipart/alternative; boundary="----=_Part_1328_17879897.1207145398560" Date: Wed, 2 Apr 2008 16:09:58 +0200 MIME-Version: 1.0 Sent to CCL by: "Marius Retegan" [marius.s.retegan[A]gmail.com] ------=_Part_1328_17879897.1207145398560 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline You could try PyMOL. On Wed, Apr 2, 2008 at 11:48 AM, jamel-eddine.meslamani*_*ulp.u-strasbg.fr < owner-chemistry%x%ccl.net> wrote: > > Sent to CCL by: jamel-eddine.meslamani[A]ulp.u-strasbg.fr > Dear cclrs, > > Actually I'd like to know if there is an open source program that could > display molecules in mol2 format and to color all of them in a one step. > I'm using linux as OS. > Thank you in advance for answers. > > Meslamani Jamelhttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_1328_17879897.1207145398560 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline You could try PyMOL.

On Wed, Apr 2, 2008 at 11:48 AM, jamel-eddine.meslamani*_*ulp.u-strasbg.fr <owner-chemistry%x%ccl.net> wrote:

Sent to CCL by: jamel-eddine.meslamani[A]ulp.u-strasbg.fr
Dear cclrs,

Actually I'd like to know if there is an open source program that could display molecules in mol2 format and to color all of them in a one step.
I'm using linux as OS.
Thank you in advance for answers.

Meslamani Jamel



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------=_Part_1328_17879897.1207145398560-- From owner-chemistry@ccl.net Wed Apr 2 12:29:00 2008 From: "snehasis banerjee ratchem2000 . gmail.com" To: CCL Subject: CCL:G: IPCM problem Message-Id: <-36617-080402102201-31442-o6QdU0kPSCDdHYuddmRVVA:server.ccl.net> X-Original-From: "snehasis banerjee" Date: Wed, 2 Apr 2008 10:21:57 -0400 Sent to CCL by: "snehasis banerjee" [ratchem2000###gmail.com] Dear all, When I using IPCM in Gaussian03 to do single point calculation for transition state and for some intermeidates, I find that the convergence of can not be reached. "the Largest difference in charges from previous cycle" either incrasing or decreasing randomly.My model is a hydrigen bond system and I am working with pt(dien) system with 32 atoms. I am using the input as: #b3lyp/GEN PSEUDO=READ SCRF=IPCM scf= tight In this situation please help me to solve the problem. From owner-chemistry@ccl.net Wed Apr 2 13:03:01 2008 From: "Nicholas Labello label030%a%umn.edu" To: CCL Subject: CCL: MOL2 program viewer Message-Id: <-36618-080402112153-21187-5GfBVh90R7Kp1Jnp6O+CIA(a)server.ccl.net> X-Original-From: Nicholas Labello Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 02 Apr 2008 09:06:35 -0500 MIME-Version: 1.0 Sent to CCL by: Nicholas Labello [label030^^umn.edu] Molden will do the trick. http://www.cmbi.ru.nl/molden/formats.html jamel-eddine.meslamani*_*ulp.u-strasbg.fr wrote: > > Sent to CCL by: jamel-eddine.meslamani[A]ulp.u-strasbg.fr > Dear cclrs, > > Actually I'd like to know if there is an open source program that > could display molecules in mol2 format and to color all of them in a > one step. > I'm using linux as OS. > Thank you in advance for answers. > > Meslamani Jamelhttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Wed Apr 2 13:42:01 2008 From: "Jim Kress ccl_nospam|kressworks.com" To: CCL Subject: CCL:G: emission spectrum Message-Id: <-36619-080402110702-17594-O94Snn+rO+ShSnqXfe7hxQ_._server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 2 Apr 2008 10:18:40 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam ~ kressworks.com] Use ORCA. It actually works. http://www.thch.uni-bonn.de/tc/orca/index.php Jim=20 > -----Original Message----- > From: Jerome Kieffer jerome.Kieffer#terre-adelie.org=20 > [mailto:owner-chemistry%ccl.net]=20 > Sent: Sunday, March 30, 2008 6:51 AM > To: Kress, Jim > Subject: CCL:G: emission spectrum >=20 >=20 > Sent to CCL by: Jerome Kieffer [jerome.Kieffer#terre-adelie.org] >=20 > > Could you please tell me how could I simulate the emission=20 > spectrum of=20 > > a system with Gaussian03? Exactly what commands should I include in=20 > > the route section in order to do this with TDDFT and CIS?=20 > In addition,=20 > > could I have the emission spectrum using GaussSum? In the=20 > G03 manual=20 > > it is not clear how one can study the S1 instead of S0 state with=20 > > TDDFT or CIS. What commands should be included in the route section=20 > > (td(Root=3D1)?) >=20 > Hello, > I think this is really difficult as S1 state generated by=20 > photo excitation (or whatever) will relax and there are=20 > little tools to allow geometry optimization of the exitated=20 > state (no analytic gradients in TDDFT). >=20 > I could be wrong ... thus very interested by the solution. >=20 > Reagards >=20 > -- > J=E9r=F4me KIEFFER : http://www.terre-adelie.org >=20 >=20 >=20 > -=3Dhis is automatically added to each message by the mailing script = =3D > To recover the email address of the author of the message,=20 > please change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/ >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl,=20 > Password: search) >=20>=20>=20 >=20 From owner-chemistry@ccl.net Wed Apr 2 14:13:00 2008 From: "DUONG PHU dtmyphu a gmail.com" To: CCL Subject: CCL: MCSCF excited state optimization make bond breaking in GAMESS Message-Id: <-36620-080402122037-24796-EHOZkF2wfyetCYtqPXVb2w(_)server.ccl.net> X-Original-From: "DUONG PHU" Date: Wed, 2 Apr 2008 12:20:33 -0400 Sent to CCL by: "DUONG PHU" [dtmyphu!A!gmail.com] Dear all I would like to locate the reactant, product and TS of the below reaction in the excited state HOOH + OH --> HOO + OH I have already success in locating all the structure in the ground state optimization I meet the problem when I try to optimize the reactant (HOOH-OH) complex in the excited state 1. In the begining part of the calculation, the output file looks well and I got 14 geometry for NSERCH=14 (14 steps), but the calculation stop at the 14th geometry because MCSCF is not converge then. When I look at the last geometry of the output file, the structure seems consist of 3 separate OH groups. So, the O-O bonding increases and breaks the bond through the optimization and the calculation may go to the wrong direction. What I expect are the convergence of the MCSCF and the output structure looks like HOOH-OH complex. 2. I confuse about choosing the active orbitals and active electrons for MCSCF calculation. I wonder whether I can solve these errors by choosing the most suitable active space or not This is my input file: $CONTRL SCFTYP=MCSCF RUNTYP=OPTIMIZE ICHARG=0 MAXIT=100 COORD=UNIQUE NZVAR=0 MULT=2 $END $SYSTEM MWORDS=120 $END $BASIS GBASIS=N31 NGAUSS=6 $END $MCSCF CISTEP=ALDET SOSCF=.FALSE. fullnr=.true. MAXIT=1000 $END $STATPT METHOD=QA NSTEP=100 STSTEP=0.01 $END $DET NCORE=10 NELS=7 NACT=7 NSTATE=4 wstate(1)=0.0,1.0 $END $GUESS GUESS=MOREAD NORB=33 $END $DATA mcscf single point energy C1 0 O 8.0 -0.8585510379 -0.6756395548 -0.0882480855 O 8.0 -0.9438055331 0.7322458924 -0.0154956352 H 1.0 -0.0175953489 0.9645677226 0.1259522268 H 1.0 -1.3945344140 -0.9445226553 0.6590686376 O 8.0 1.8274833255 0.0282545293 0.0265415831 H 1.0 1.2111157267 -0.6989320022 -0.1674037635 $END The ouput file contains: BEGINNING GEOMETRY SEARCH POINT NSERCH= 14 ... O 8.0 -0.7575197144 -1.3395157854 0.0420941149 O 8.0 -0.9320424674 1.3053406640 0.1489054020 H 1.0 0.0268559396 1.2443405186 0.0219127967 H 1.0 -1.5763699597 -1.0810734623 0.4897268742 O 8.0 1.7784966539 0.0552824933 -0.0992671117 H 1.0 1.2846922663 -0.7784004962 -0.0629571128 ... ... 999 -226.109386045 -0.000000003 0.242979 11 1 9.245E-03 1********* *** -226.109386048 -0.000000003 0.242979 11 1 9.245E-03 1********* EXCESSIVE NUMBER OF ITERATIONS... Any suggestion to solve this problem are highly appreciated From owner-chemistry@ccl.net Wed Apr 2 14:51:01 2008 From: "Allen Richon abrichon!=!netsci.org" To: CCL Subject: CCL: Early Comp groups in industry Message-Id: <-36621-080402140347-9298-ej/BuVQa6K54IBtIFaa5CQ===server.ccl.net> X-Original-From: Allen Richon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Wed, 2 Apr 2008 13:13:17 -0400 Mime-Version: 1.0 (Apple Message framework v624) Sent to CCL by: Allen Richon [abrichon]![netsci.org] Greetings: I am in the process of collecting data on the start of computational chemistry within the chemical industry (pharma, materials, chemicals, ag, and so on). I know that Abbott and Smith Kline initiated their efforts in the late 60's/early 70's, Lilly at about the same time, DuPont, Merck, Rohm & Haas, Upjohn, Syntex in the early/mid-70's, and so on. Can the members of the list provide starting points for other groups? I will be happy to post the summary if people would like to respond to me directly. Thanks! Allen Richon abrichon##netsci.org From owner-chemistry@ccl.net Wed Apr 2 15:27:00 2008 From: "Pablo Englebienne pablo.englebienne===mcgill.ca" To: CCL Subject: CCL: MOL2 program viewer Message-Id: <-36622-080402121857-23495-E5tY7DZ828U7hiJNIq1vMQ^server.ccl.net> X-Original-From: Pablo Englebienne Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 02 Apr 2008 11:41:53 -0400 MIME-Version: 1.0 Sent to CCL by: Pablo Englebienne [pablo.englebienne.{:}.mcgill.ca] My choice would be PyMol: http:///www.pymol.org. Although not completely free (it's user-sponsored, providing support and documentation), it's open source, scriptable and with lots of documentation available online. The quality of the images generated with it is the best I have seen so far. Cheers! -- Pablo Englebienne, PhD Student, Moitessier research group Department of Chemistry, McGill University 801 Sherbrooke Street West Otto Maass bldg, room 206 H3A 2K6 Montréal, Québec, Canada Tel (514) 398-5501 Fax (514) 398-2382 "Progress is made by lazy men looking for easier ways to do things." - Robert A. Heinlein jamel-eddine.meslamani*_*ulp.u-strasbg.fr wrote: > > Sent to CCL by: jamel-eddine.meslamani[A]ulp.u-strasbg.fr > Dear cclrs, > > Actually I'd like to know if there is an open source program that > could display molecules in mol2 format and to color all of them in a > one step. > I'm using linux as OS. > Thank you in advance for answers. > > Meslamani Jamelhttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Wed Apr 2 17:43:01 2008 From: "Soren Eustis soren~!~jhu.edu" To: CCL Subject: CCL:G: Checkpoint files Message-Id: <-36623-080402172353-20229-ePFBa1PPFjdrDf5ZEy1/lA|*|server.ccl.net> X-Original-From: "Soren Eustis" Content-language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0069_01C894DD.DC73D0C0" Date: Wed, 2 Apr 2008 16:23:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren-.-jhu.edu] This is a multipart message in MIME format. ------=_NextPart_000_0069_01C894DD.DC73D0C0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit I am having trouble reading in a checkpoint generated on a 64-bit linux computer running G03 via webmo. When I download the checkpoint file Gaussview and my other visualization programs are unable to open it. I have tried formchk and unix2dos followed by formchk (as I am reading it on a windows system). I have worked with checkpoint files many times in the past. The difference here is I am working on a new computer and the new elements are the 64-bit cpu and the Linux operating system. Am I dealing with a unix to dos issue? If so, why doesn't unix2dos work? Is this somehow a 64-bit issue? Anyone encounter this before? Soren Soren N. Eustis Doctoral Candidate Department of Chemistry Johns Hopkins University Remsen Hall 3400 North Charles Street Baltimore, MD 21218 410-516-4675 (office) 410-925-5167 (cell) 410-516-8420 (fax) soren .. jhu.edu ------=_NextPart_000_0069_01C894DD.DC73D0C0 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

I am having trouble reading in a checkpoint = generated on a 64-bit linux computer running G03 via webmo.  When I download the checkpoint file Gaussview and my other visualization programs are unable = to open it. I have tried formchk and unix2dos followed by formchk (as I am = reading it on a windows system).  I have worked with checkpoint files many = times in the past.  The difference here is I am working on a new computer = and the new elements are the 64-bit cpu and the Linux operating = system.

 

Am I dealing with a unix to dos issue?  If so, = why doesn’t unix2dos work?  Is this somehow a 64-bit issue?  =

 

Anyone encounter this before?

 

Soren

 

Soren N. Eustis

Doctoral Candidate

Department of Chemistry

Johns Hopkins University

Remsen Hall

3400 North Charles Street

Baltimore, MD 21218

410-516-4675 (office)

410-925-5167 (cell)

410-516-8420 (fax)

soren .. jhu.edu

 

------=_NextPart_000_0069_01C894DD.DC73D0C0-- From owner-chemistry@ccl.net Wed Apr 2 18:20:00 2008 From: "David A. Case case[A]scripps.edu" To: CCL Subject: CCL: ANNOUNCE: Release of AmberTools, version 1.0 Message-Id: <-36624-080402173851-21685-uxeua0kMYjpkk31niygfAQ**server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 2 Apr 2008 09:49:20 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case=-=scripps.edu] We are proud to annouce the release of AmberTools. AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular mechanics investigations (using NAB), but which are restricted to gas-phase or generalized Born solvent models. AmberTools currently consists of four main codes that were previously released separately, and one new one: nucleic acid builder (NAB) http://www.scripps.edu/case/nab.html antechamber http://amber.scripps.edu/antechamber ptraj http://www.chpc.utah.edu/~cheatham/software.html tleap and xleap http://amber.scripps.edu sleap New: replaces and expands tleap These programs may also be of interest outside the Amber community. For example, antechamber can create CHARMM-formatted parameter files, and ptraj can analyze CHARMM trajectories. We expect that AmberTools will be dynamic, and change and grow over time. This initial release consists of programs that have previously been part of Amber (including LEaP, antechamber and ptraj), along with NAB (Nucleic Acid Builder), which has been released separately. Each of these packages (except for sleap) has been in use for a long time. They are certainly not bug-free, but you should be able to rely upon them in many circumstances. These are the latest releases of these programs, and collect in one place codes that we have been distributing for some time. The programs here are mostly released under the GNU General Public License (GPL). A few components are included that are in the public domain or which have other, open-source, licenses. We hope to add new functionality to AmberTools as additional programs become available. If you have suggestions for what might be added, please contact us. (CHARMM users might note that antechamber can prepare parameters in CHARMM format, and ptraj can read and analyze CHARMM trajectories.) To obtain AmberTools, go to: http://ambermd.org/#AmberTools ...dave case (for the Amber development team) From owner-chemistry@ccl.net Wed Apr 2 19:21:01 2008 From: "Vlad vvv900_-_anusf.anu.edu.au" To: CCL Subject: CCL: MOL2 program viewer Message-Id: <-36625-080402190332-18947-GYHusExZavBa6ZJ3UjxeaA__server.ccl.net> X-Original-From: Vlad Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 03 Apr 2008 09:29:29 +1100 MIME-Version: 1.0 Sent to CCL by: Vlad [vvv900()anusf.anu.edu.au] Hi Meslamani, > Actually I'd like to know if there is an open source program that could > display molecules in mol2 format and to color all of them in a one step. > I'm using linux as OS. You might want to try JMolEditor: http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html Regards, Vlad From owner-chemistry@ccl.net Wed Apr 2 23:48:00 2008 From: "Diego Moreno dvmorenor{=}unal.edu.co" To: CCL Subject: CCL: similarity of different molecules Message-Id: <-36626-080402234351-29471-+suARBEjeHbplMzvJxrcQA!^!server.ccl.net> X-Original-From: "Diego Moreno" Date: Wed, 2 Apr 2008 23:43:46 -0400 Sent to CCL by: "Diego Moreno" [dvmorenor~~unal.edu.co] Sent to CCL by: "JunJun Liu" [ljjlp03\a/gmail.com] Hello everybody, I want to know how similar two different molecules are. Does anybody know how to do this? Any suggestions regarding algorithms or softwares are highly appreciated! Thanks in advance! Junjun Hi Junjun If you are interested in compare molecules or in algorithms designed to know hwo different two molecules are, you will find a lot of them that requiere to align the molecular skeletons. An interesting option is a program called TARIS, that is designed to compare molecules according to their molecular electrostatic potentials. It's main advantage is that you don't need to do any kind of alingment. You just need one .cube file with the MEP information of the molecules. The program uses a graph theoretical approach that make is use really efficient. You may find this program at http://taris.sourceforge.net. In addition I'm sending you the paper where this method was published. Best regards, - ___ ___ ___ /\ \ /\ \ /\ \ /::\ \ /::\ \ \:\ \ Diego Moreno /:/\:\__\\:\:\__\ /::\__\ \:\:\/__/ \::/ //:/\/__/ Grupo de Qumica Terica \::/ / /:/ //:/ / Universidad Nacional de Col.\/__/ \/__/ \/_/