From owner-chemistry@ccl.net Sun Mar 9 01:59:00 2008 From: "Matt James Ketterer mkettere- -iupui.edu" To: CCL Subject: CCL: Running large proteins in Tinker Message-Id: <-36462-080307130127-6722-0v0l2ezzWJBysiMbb23pPQ[#]server.ccl.net> X-Original-From: "Matt James Ketterer" Date: Fri, 7 Mar 2008 13:01:24 -0500 Sent to CCL by: "Matt James Ketterer" [mkettere]|[iupui.edu] Hello all. I am a student currently new to using Tinker. I am trying to use the Newton program to minimize my protein, although the Hessian is too large for the program as installed. I know that I can recompile the source code to specify a larger number of Hessians, which I am in the process of doing, but I was wondering if it is possible to simply use the newly made coordinate file (xyz_2) a second or third time to get the RMS down to a suitable convergence. I tried doing this through the GUI and even renaming the file but it reverts back to the "increase MaxHESS" message. Is that my only option? From owner-chemistry@ccl.net Sun Mar 9 05:12:01 2008 From: "Mohamed Imran imranpkm!=!gmail.com" To: CCL Subject: CCL: gamess error message ($DET keyword) Message-Id: <-36463-080308134402-9208-5zeSk1NdbwDpR5cdakfQfA:server.ccl.net> X-Original-From: Mohamed Imran Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 08 Mar 2008 22:52:53 +0530 MIME-Version: 1.0 Sent to CCL by: Mohamed Imran [imranpkm-*-gmail.com] Generally, problem with input line has been in the lengthier line. You can make the $DET in two lines (a return key after ISTSYM=1). You can make a try. regards Imran Predhanekar sherin falah shireenfalah(0)hotmail.com wrote: > Sent to CCL by: "sherin falah" [shireenfalah^_^hotmail.com] > Dear CCL users, > I am trying to submit some calculations using gamess us but my jobs crashed always. > My input files looks like: > > $CONTRL SCFTYP=MCSCF MULT=1 RUNTYP=ENERGY $END > $FORCE METHOD=ANALYTIC $END > $MCSCF CISTEP=ALDET MAXIT=480 FULLNR=.T. $END > $DET GROUP=1 NCORE=18 NACT=6 NELS=6 ISTSYM=1 NSTATE=4 SZ=0 WSTATE(1)=1,1,0,0 $END > $STATPT NSTEP=120 $END > > The error message I got is : > > INCORRECT DATA VALUE FOUND > **** ERROR READING INPUT GROUP $DET ***** > THE PROBLEM IS WITH THIS INPUT LINE, NEAR THE X MARKER > $STATPT NSTEP=120 $END > X > > I am sure that the error is not in the "STATPT" keyword because I got similar message whatever keywords I put in the line after the $DET line. > I tried to rewrite the file again to come over any hidden format problem but this did not help. I have no clue what is going wrong here. > Any help would be really appreciated. > Thanks in advance. > Best regards, > Shireen Falah> > > > From owner-chemistry@ccl.net Sun Mar 9 05:54:00 2008 From: "Dimitri Svistunenko svist : essex.ac.uk" To: CCL Subject: CCL: Isotropic Fermi Contact Couplings Message-Id: <-36464-080309055121-27664-8PT+BPRNHDBhRLgHHFbzHA||server.ccl.net> X-Original-From: "Dimitri Svistunenko" Date: Sun, 9 Mar 2008 05:51:17 -0400 Sent to CCL by: "Dimitri Svistunenko" [svist|essex.ac.uk] Why is it, the couplings are printed in the output file for small molecules but are not for the structures of a size of about 200 atoms. We managed of get the anisotropic components by using PROP=EPR, but the isotropic components are still not in the output. It seems that ReadAtoms might be required as an NMR option for calculating specific atons only (specified at the end of input file). But this keyword, NMR=ReadAtons returns an erroe 1 sec after statr with an error in the first line. Basically, I cannot see anything wrong with the input file, but maybe you could: %chk=tptog.chk %mem=256mb # B3LYP/6-31G* SP NMR=ReadAtoms SP calculation; tyr and peptide optimised together 0 2 C C 1 1.51926 O 2 1.22113 1 122.77328 N 2 1.38393 1 114.95671 3 179.83033 C 4 1.45852 2 121.6391 1 -166.6051 C 5 1.54617 4 113.69401 2 -123.5313 O 6 1.22606 5 120.57219 4 -162.35476 C 5 B1 4 A1 2 D1 C 8 B2 5 A2 4 D2 * * * D19 118.7436 D20 -0.4311 27-32 41 From owner-chemistry@ccl.net Sun Mar 9 22:53:00 2008 From: "Deskins, Nathaniel A nathaniel.deskins^pnl.gov" To: CCL Subject: CCL: VASP:how to calculate phonon spectrum ? Message-Id: <-36465-080307193628-10007-dDy4Gy3Qu10Luiyeg/q9Ng[a]server.ccl.net> X-Original-From: "Deskins, Nathaniel A" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 7 Mar 2008 15:36:02 -0800 MIME-Version: 1.0 Sent to CCL by: "Deskins, Nathaniel A" [nathaniel.deskins[#]pnl.gov] VASP only allows the calculation of the frequencies at the gamma point. See the manual (IBRION =3D 5) for this. You can use the following program with VASP to calculate the phonon spectrum. http://wolf.ifj.edu.pl/phonon/ Aaron =20 -----Original Message----- > From: owner-chemistry**ccl.net [mailto:owner-chemistry**ccl.net]=20 Sent: Thursday, March 06, 2008 5:39 PM To: Deskins, Nathaniel A Subject: CCL: VASP:how to calculate phonon spectrum ? Sent to CCL by: "Guanna Li" [gnli*dicp.ac.cn] Dear CCLer, dose anybody have some experience in calculating phonon spectrum by VASP? could anybody please give me an example of the input file or recommend another opensource process ? Thanks in advance! =09 -------------- 2008-03-07 Best wishes =20 Guanna Li Email: gnli]^[dicp.ac.cn -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20http://www.ccl.net/spammers.txt