From owner-chemistry@ccl.net Tue Apr 1 01:04:01 2008 From: "Isabelle Navizet navizet#,#univ-mlv.fr" To: CCL Subject: CCL: Modifying Tinker parameter sets for zinc ion (amber99 or charm27) Message-Id: <-36604-080401000818-21061-cbXAvwQ4KVSSmkz4khgnVA[]server.ccl.net> X-Original-From: Isabelle Navizet Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 01 Apr 2008 11:11:02 +0800 Mime-Version: 1.0 Sent to CCL by: Isabelle Navizet [navizet++univ-mlv.fr] Hello Matt, I see Zn+2 in amber99.prm. The atom type of Tinker is 2010. Did you put this atom type in your .xyz file ? You should then use the amber99.prm library. In charmm27.prm, the atom type is 115. I hope this help. Isabelle Navizet On Mon, 2008-03-31 at 20:32 -0400, Matt James Ketterer mkettere]![iupui.edu wrote: > Sent to CCL by: "Matt James Ketterer" [mkettere^^^iupui.edu] > Hello all. > I am trying to run the various programs in Tinker on zinc metallo betalactamase, and am having trouble reading or manually inserting the zinc ion (or any metal ion) into the active site to run calculations. I have tried editing of xyz files manually to include the metal ion parameter set number but Tinker still would not read it or perform calculations. I don't know if the parameter sets which include the zinc or Mg+ or other ions (amber99 or charmm27)have been implemented in Tinker or if the current version of the program is equipped to handle all of the atoms in the parameter sets. Currently I have tried the amber99 and charmm27 parameter sets, and have manually entered the coordinates to the xyz file with the proper format and atom number but to no avail. I have also tried to use the xyzedit.x program to insert the zinc ion, also without progress. Also, I wasn't sure if the sequence file generated with the protein file needs to include a general metal ion code such a! > s MTL to recognize the metal. Any help would be greatly appreciated. > Thanks > Matt Ketterer > mkettere!^!iupui.edu> > -- ------------------------------------------------------------------------ Isabelle Navizet (Soury-Lavergne) add 1: Beijing Normal University, Department of Chemistry add 2: Laboratoire de Chimie Theorique Universite Paris-Est Marne la Vallee email : navizet at univ-mlv.fr From owner-chemistry@ccl.net Tue Apr 1 09:03:01 2008 From: "Jones de Andrade johannesrs]![gmail.com" To: CCL Subject: CCL: Gamess linking problem Message-Id: <-36605-080401014534-16651-qijkChqsSs1VzCRETZ2PMw||server.ccl.net> X-Original-From: "Jones de Andrade" Content-Type: multipart/alternative; boundary="----=_Part_10442_9184495.1207022174605" Date: Tue, 1 Apr 2008 00:56:14 -0300 MIME-Version: 1.0 Sent to CCL by: "Jones de Andrade" [johannesrs_+_gmail.com] ------=_Part_10442_9184495.1207022174605 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline 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 ------=_Part_10442_9184495.1207022174605 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline 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
------=_Part_10442_9184495.1207022174605-- From owner-chemistry@ccl.net Tue Apr 1 09:38:00 2008 From: "Guanna Li gnli()dicp.ac.cn" To: CCL Subject: CCL:G: emission spectrum Message-Id: <-36606-080331223249-5974-FJWn9HttILgkWwuv9rFtXg^-^server.ccl.net> X-Original-From: "Guanna Li" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Tue, 1 Apr 2008 10:31:28 +0800 Mime-Version: 1.0 Sent to CCL by: "Guanna Li" [gnli%a%dicp.ac.cn] Dear Raji, You talked about the step to calculate emission spectrum. If gaussianview can draw the spectrum directly? or should we need other program to deal with the data? Thank you! Best wishes Guanna Li Best wishes Guanna Li From owner-chemistry@ccl.net Tue Apr 1 13:00:01 2008 From: "Francisco Hernandez-Guzman fhernandez ~ accelrys.com" To: CCL Subject: CCL: Titration curves using Generalized Born Model Message-Id: <-36607-080401122010-31000-/Qz+Uktv3h07QkbiwYlZ3g..server.ccl.net> X-Original-From: Francisco Hernandez-Guzman Content-type: text/plain; charset=US-ASCII Date: Tue, 1 Apr 2008 09:19:05 -0700 MIME-Version: 1.0 Sent to CCL by: Francisco Hernandez-Guzman [fhernandez+*+accelrys.com] Dear Maurizzio, Perhaps not a free option, but Accelrys has developed a new pK predictor (generates theoretical titration curves, estimates pI, estimates folding energy as a function of pH, protonates/deprotonates titratable residues on a selected pH, and more) based on the Generalized Born solvation model. Given the use of the GB model, the algorithm is particularly fast. We are in the process of writing the paper for publication, but all of our validation studies show great correlation to experimental data, even in cases were large pK shifts occur, and also where shifts are induced due to ligand binding. If you're interested please feel free to contact me directly so I can provide you with more information. Kind regards, Francisco ---------------------------------------------------------------------- Francisco G. Hernandez-Guzman, Ph.D. Sr. Solutions Scientist, Protein Modeling, Simulations and X-ray - USA Accelrys Inc. (http://www.accelrys.com) Office: (858) 799 - 5606 Fax: (858) 799 - 5100 Mobile: (858) 361 - 3020 E-mail: fhernandez##accelrys.com --------------------------------------------------------------------- Accelrys support: 1-800-756-4674 E-mail: support##accelrys.com --------------------------------------------------------------------- "Maurizzio m.argonni,gmail.c om" To " Sent by: cc owner-chemistry##c cl.net Subject CCL: Titration curves using Generalized Born Model 03/31/2008 07:51 AM Please respond to "CCL Subscribers" Dear CCL'ers: I would like to know if any of you is aware of free software that allows the computation of theoretical titration curves of ionizable residues in proteins using a Generalized Born approach rather than the more common Poisson-Boltzmann approach implemented in programs like UHBD and Delphi. Any help is greatly appreciated. Maurizzio Click here to report this email as spam. From owner-chemistry@ccl.net Tue Apr 1 14:20:00 2008 From: "Oleksandr nablaoblada^yahoo.com" To: CCL Subject: CCL: fullerene C82 symmetric coordinates? Message-Id: <-36608-080401105911-21555-4PzlZAuaHsQwQECSAKDaxA{}server.ccl.net> X-Original-From: Oleksandr Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 1 Apr 2008 06:58:58 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Oleksandr [nablaoblada*o*yahoo.com] Hi, Does anybody have the fullerene C82 symmetric coordinates for 9 isomers? Please don't refer to the link http://www.ccl.net/cca/data/fullerenes/index.shtml because C82 is not listed there. The only coordinates I found on http://www.cochem2.tutkie.tut.ac.jp/Fuller/higher/higherE.html and they were "preoptimized" and therefore not symmetric. Thank you Oleksandr ____________________________________________________________________________________ You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost. http://tc.deals.yahoo.com/tc/blockbuster/text5.com From owner-chemistry@ccl.net Tue Apr 1 22:13:01 2008 From: "Don Steiger sd00_2002,yahoo.com" To: CCL Subject: CCL: Practical optimization of FMM / Fast Multipole Method (electrostatics) Message-Id: <-36609-080331225746-9043-pU1W81ccLlMQcAjzV1T3fA|-|server.ccl.net> X-Original-From: Don Steiger Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-579737705-1207015054=:19612" Date: Mon, 31 Mar 2008 18:57:34 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Don Steiger [sd00_2002^yahoo.com] --0-579737705-1207015054=:19612 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit "Andrey.Bliznyuk++anu.edu.au" wrote: Sent to CCL by: Andrey.Bliznyuk ~~ anu.edu.au Hi, > My question is, how is optimization of FMM done in practice? > Are analytical gradients calculated? And if so, has the gradient > function been derived and made publicly available somewhere? > Or does one use a non-gradient based approach with this function? If I understand correctly, you want to do geometry optimisation using FMM for coulomb interactions. Yes, analytical gradients of FMM are easily obtainable. This is just gradients of the Legendre polynomials which are, naturally, Legendre polynomials. The gradient of the surface that an fmm algorithm produces will not be an approximation to the gradient of the actual surface, even if the fmm is generating very good approximations for the Coulombic interactions. --------------------------------- You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost. --0-579737705-1207015054=:19612 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

"Andrey.Bliznyuk++anu.edu.au" <owner-chemistry/./ccl.net> wrote:

Sent to CCL by: Andrey.Bliznyuk ~~ anu.edu.au
Hi,

> My question is, how is optimization of FMM done in practice?
> Are analytical gradients calculated? And if so, has the gradient
> function been derived and made publicly available somewhere?
> Or does one use a non-gradient based approach with this function?

If I understand correctly, you want to do geometry optimisation using
FMM for coulomb interactions. Yes, analytical gradients of FMM are
easily obtainable. This is just gradients of the Legendre polynomials which
are, naturally, Legendre polynomials.

The gradient of the surface that an fmm algorithm produces will not be an approximation to the gradient of the actual surface, even if the fmm is generating very good approximations for the Coulombic interactions.

You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost. --0-579737705-1207015054=:19612--