From owner-chemistry@ccl.net Tue Aug 23 13:35:23 2005 From: "CCL" To: CCL Subject: CCL: GAMESS restart Message-Id: <-28986-050823133443-29857-sJTYeKniThUXNerGpwThRw ~~ server.ccl.net> X-Original-From: "William Wei" content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5A808.F0F4A7DC" MIME-Version: 1.0 Sent to CCL by: "William Wei" This is a multi-part message in MIME format. ------_=_NextPart_001_01C5A808.F0F4A7DC Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable X-NAIMIME-Disclaimer: 1 X-NAIMIME-Modified: 1 > Hi Fellows, >=20 > I just started to use GAMESS for a structure optimixation. Because > the time and MAXIT issue, GAMESS stopped without writing > coordinates(at least I did not find). So I am wondering that what > option I need to use for restart GAMESS with my geometry optimization? > There is a ./scr/.dat file in my home directory. Anybody could help > me to restart the job? >=20 > Thanks in advance, > William >=20 > -------------------------------- > William Wei, Ph.D. > Computational Chemist > Lorus Therapeutics Inc. > 2 Meridian Road > Toronto, On, M9W 4Z7 > 416-798-1200 Ext. 374 > wwei ~~ lorusthera.com >=20 >=20 This message contains CONFIDENTIAL INFORMATION intended solely for the us= e of the addressee(s) named above.=0AAny review, disclosure, distribution= , copying or use of the information by others is strictly prohibited. =0A= If you have received this message in error, please advise the sender by i= mmediate reply and delete the original message.=0A ------_=_NextPart_001_01C5A808.F0F4A7DC Content-Type: text/HTML; charset="us-ascii" Content-Transfer-Encoding: quoted-printable X-NAIMIME-Disclaimer: 1 X-NAIMIME-Modified: 1 Hi Fellows,

I just started to use GAMESS for a struc= ture optimixation. Because the time and MAXIT issue, GAMESS stopped= without writing coordinates(at least I did not find). So I am wond= ering that what option I need to use for restart GAMESS with my geometry = optimization? There is a ./scr/.dat file in my home directory= =2E Anybody could help me to restart the job?

Thanks in advance,
William

--------------------------------
William Wei, Ph.D.
Computational Chemist
Lorus Therapeutics Inc.
2 Meridian Road
Toronto, On, M9W 4Z7
416-798-1200 Ext. 374
wwei ~~ lorusthera.com

This message contains CONFIDENTIAL INFORMATION intended solely for the us= e of the addressee(s) named above.
=0AAny review, disclosure, distribu= tion, copying or use of the information by others is strictly prohibited.=
=0AIf you have received this message in error, please advise the sen= der by immediate reply and delete the original message.
=0A

------_=_NextPart_001_01C5A808.F0F4A7DC-- From owner-chemistry@ccl.net Tue Aug 23 14:03:33 2005 From: "CCL" To: CCL Subject: CCL: GAMESS restart Message-Id: <-28987-050823140300-7716-sJTYeKniThUXNerGpwThRw+*+server.ccl.net> X-Original-From: "Compchem List" content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5A80C.E436B392" MIME-Version: 1.0 Sent to CCL by: "Compchem List" This is a multi-part message in MIME format. ------_=_NextPart_001_01C5A80C.E436B392 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable X-NAIMIME-Disclaimer: 1 X-NAIMIME-Modified: 1 > Hi Fellows, >=20 > I just started to use GAMESS for a structure optimixation. Because > the time and MAXIT issue, GAMESS stopped without writing > coordinates(at least I did not find). So I am wondering that what > option I need to use for restart GAMESS with my geometry optimization? > There is a ./scr/.dat file in my home directory. Anybody could help > me to restart the job? >=20 > Thanks in advance, > William >=20 > -------------------------------- > William Wei, Ph.D. > Computational Chemist > Lorus Therapeutics Inc. > 2 Meridian Road > Toronto, On, M9W 4Z7 > 416-798-1200 Ext. 374 > wwei+*+lorusthera.com >=20 >=20 This message contains CONFIDENTIAL INFORMATION intended solely for the us= e of the addressee(s) named above.=0AAny review, disclosure, distribution= , copying or use of the information by others is strictly prohibited. =0A= If you have received this message in error, please advise the sender by i= mmediate reply and delete the original message.=0A ------_=_NextPart_001_01C5A80C.E436B392 Content-Type: text/HTML; charset="us-ascii" Content-Transfer-Encoding: quoted-printable X-NAIMIME-Disclaimer: 1 X-NAIMIME-Modified: 1 Hi Fellows,

Thanks in advance,
William

--------------------------------
William Wei, Ph.D.
Computational Chemist
Lorus Therapeutics Inc.
2 Meridian Road
Toronto, On, M9W 4Z7
416-798-1200 Ext. 374
wwei+*+lorusthera.com

------_=_NextPart_001_01C5A80C.E436B392-- From owner-chemistry@ccl.net Tue Aug 23 17:44:12 2005 From: "CCL" To: CCL Subject: CCL: g0 error: exceedes maximum nsteps Message-Id: <-28988-050823151211-914-UNx87URgxW7cVfCZQnK2iA_-_server.ccl.net> X-Original-From: Eric Hu Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: Eric Hu Hi CCLers I have performed a TS search at various level of theories (pm3, hf and b3lyp). They all end up without converging and complain the number of nstep (=276) is reached. For pm3 level, I redid the calculation three times with the input geometry from the previous unfinished run and still got the same problem. I wonder if this is a suggestion that there is no TS nearby at the suggested geometry. Also I wonder if I can change NSTEP to a bigger number. Thanks. Eric From owner-chemistry@ccl.net Tue Aug 23 22:53:18 2005 From: "CCL" To: CCL Subject: CCL: parameters for Al in GAMESS+Tinker Message-Id: <-28989-050823224555-3811-sJTYeKniThUXNerGpwThRw-&-server.ccl.net> X-Original-From: "Baltrusaitis, Jonas" content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Sent to CCL by: "Baltrusaitis, Jonas" Hello, while trying to proceed with geometry optimization using Al atoms containing cluster with GAMESS+Tinker code MM/QM procedure I get error message: Undefined or Illegal Atom Types : and all my Al atoms are marked as undefined. I built a custom parameter set from literature references using text editor, but it looks like Tinker doesn't recognize it as valid. I nitially it gave same error when I tried to use mm2 parameter file, but the new one definetile has Al atoms in it. What can be wrong? Full output is given below: INPUT CARD> !Al14O22 test INPUT CARD> $CONTRL SCFTYP=RHF RUNTYP=optimize MULT=1 ICHARG=-2 NOSYM=1 INPUT CARD> COORD=TINKER NZVAR=114 UNITS=ANGS MAXIT=200 $END INPUT CARD> $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 DIFFSP=.t. $END INPUT CARD> $GUESS GUESS=HUCKEL $END INPUT CARD> $intgrl qfmm=.f. $end INPUT CARD> $STATPT opttol= .0005 nprt=-2 npun=-1 NSTEP=200 INPUT CARD> $ZMAT DLC=.T. AUTO=.T. $END INPUT CARD> $SCF DIRSCF=.T. NPUNCH=2 $END INPUT CARD> $SYSTEM TIMLIM=99999999 MEMORY=30000000 $END INPUT CARD> $TINXYZ INPUT CARD> 40 data MM2 parameters INPUT CARD> 1 O -1.383000 4.139000 9.781000 6 5 39 INPUT CARD> 2 AL -2.381000 4.124000 4.548000 0 14 13 10 INPUT CARD> 3 AL 2.369000 4.124000 4.548000 0 16 15 12 INPUT CARD> 4 AL 2.373000 1.375000 6.233000 0 15 11 8 INPUT CARD> 5 AL -2.347000 4.122000 8.195000 0 20 19 18 1 INPUT CARD> 6 AL 2.313000 4.121000 8.154000 0 22 21 9 38 INPUT CARD> 7 AL -0.004000 2.749000 6.705000 0 11 20 17 9 INPUT CARD> 8 O 3.820000 1.375000 7.547000 6 4 23 INPUT CARD> 9 O 1.648000 2.631000 7.547000 6 7 6 INPUT CARD> 10 O -1.451000 2.749000 5.391000 6 2 24 INPUT CARD> 11 O 0.721000 1.493000 5.391000 6 4 7 INPUT CARD> 12 O 0.718000 4.006000 5.391000 6 3 25 INPUT CARD> 13 O -1.659000 5.616000 5.391000 6 2 25 INPUT CARD> 14 O -4.032000 4.006000 5.391000 6 2 26 INPUT CARD> 15 O 3.299000 2.749000 5.391000 6 3 4 INPUT CARD> 16 O 3.091000 5.616000 5.391000 6 3 27 INPUT CARD> 17 O -0.930000 1.375000 7.547000 6 24 7 INPUT CARD> 18 O -3.310000 5.498000 7.547000 6 28 5 INPUT CARD> 19 O -3.102000 2.631000 7.547000 6 29 5 INPUT CARD> 20 O -0.730000 4.242000 7.547000 6 7 5 INPUT CARD> 21 O 1.439000 5.498000 7.547000 6 30 6 INPUT CARD> 22 O 4.020000 4.242000 7.547000 6 23 6 INPUT CARD> 23 AL 4.746000 2.749000 6.705000 0 34 22 8 INPUT CARD> 24 AL -2.377000 1.375000 6.233000 0 10 31 17 INPUT CARD> 25 AL -0.008000 5.498000 6.233000 0 32 13 12 35 INPUT CARD> 26 AL -4.758000 5.498000 6.233000 0 14 33 36 INPUT CARD> 27 AL 4.742000 5.498000 6.233000 0 16 34 37 INPUT CARD> 28 AL -2.385000 6.873000 6.705000 0 33 35 18 INPUT CARD> 29 AL -4.754000 2.749000 6.705000 0 31 36 19 INPUT CARD> 30 AL 2.365000 6.873000 6.705000 0 32 37 21 INPUT CARD> 31 O -4.029000 1.493000 5.391000 6 24 29 INPUT CARD> 32 O 0.918000 6.873000 5.391000 6 25 30 INPUT CARD> 33 O -3.832000 6.873000 5.391000 6 26 28 INPUT CARD> 34 O 5.468000 4.006000 5.391000 6 27 23 INPUT CARD> 35 O -0.733000 6.755000 7.547000 6 25 28 INPUT CARD> 36 O -5.480000 4.242000 7.547000 6 26 29 INPUT CARD> 37 O 4.017000 6.755000 7.547000 6 27 30 INPUT CARD> 38 O 1.449000 4.152000 9.780000 6 6 39 ..... DONE SETTING UP THE RUN ..... ---- QMMM procedure is ON ---- ############################################################################## ############################################################################## ## ## ## TINKER --- Software Tools for Molecular Design ## ## ## ## Version 3.6 February 1998 ## ## ## ## Copyright (c) Jay William Ponder 1990-1998 ## ## All Rights Reserved ## ## ## ############################################################################## ############################################################################## ---------------------------------------------------------------------------- Cartesian Coordinates of Atoms in Bulk Model (ANGS) ---------------------------------------------------------------------------- 40 DATA 1 O -1.383000 4.139000 9.781000 6 5 39 2 AL -2.381000 4.124000 4.548000 0 10 13 14 3 AL 2.369000 4.124000 4.548000 0 12 15 16 4 AL 2.373000 1.375000 6.233000 0 8 11 15 5 AL -2.347000 4.122000 8.195000 0 1 18 19 20 6 AL 2.313000 4.121000 8.154000 0 9 21 22 38 7 AL -0.004000 2.749000 6.705000 0 9 11 17 20 8 O 3.820000 1.375000 7.547000 6 4 23 9 O 1.648000 2.631000 7.547000 6 6 7 10 O -1.451000 2.749000 5.391000 6 2 24 11 O 0.721000 1.493000 5.391000 6 4 7 12 O 0.718000 4.006000 5.391000 6 3 25 13 O -1.659000 5.616000 5.391000 6 2 25 14 O -4.032000 4.006000 5.391000 6 2 26 15 O 3.299000 2.749000 5.391000 6 3 4 16 O 3.091000 5.616000 5.391000 6 3 27 17 O -0.930000 1.375000 7.547000 6 7 24 18 O -3.310000 5.498000 7.547000 6 5 28 19 O -3.102000 2.631000 7.547000 6 5 29 20 O -0.730000 4.242000 7.547000 6 5 7 21 O 1.439000 5.498000 7.547000 6 6 30 22 O 4.020000 4.242000 7.547000 6 6 23 23 AL 4.746000 2.749000 6.705000 0 8 22 34 24 AL -2.377000 1.375000 6.233000 0 10 17 31 25 AL -0.008000 5.498000 6.233000 0 12 13 32 35 26 AL -4.758000 5.498000 6.233000 0 14 33 36 27 AL 4.742000 5.498000 6.233000 0 16 34 37 28 AL -2.385000 6.873000 6.705000 0 18 33 35 29 AL -4.754000 2.749000 6.705000 0 19 31 36 30 AL 2.365000 6.873000 6.705000 0 21 32 37 31 O -4.029000 1.493000 5.391000 6 24 29 32 O 0.918000 6.873000 5.391000 6 25 30 33 O -3.832000 6.873000 5.391000 6 26 28 34 O 5.468000 4.006000 5.391000 6 23 27 35 O -0.733000 6.755000 7.547000 6 25 28 36 O -5.480000 4.242000 7.547000 6 26 29 37 O 4.017000 6.755000 7.547000 6 27 30 38 O 1.449000 4.152000 9.780000 6 6 39 39 C 0.037000 4.164000 10.246000 1 1 38 40 40 O 0.038000 4.203000 11.645000 6 39 ---------------------------------------------------------------------------- parameters C:/WinGAMESS/MMparameters/alumina $END List of InActive Atoms for Energy Calculations : Parameter file unit number 1 Undefined or Illegal Atom Types : Type Atom Number Atom Type Atom 2 0 Atom 3 0 Atom 4 0 Atom 5 0 Atom 6 0 Atom 7 0 Atom 23 0 Atom 24 0 Atom 25 0 Atom 26 0 Atom 27 0 Atom 28 0 Atom 29 0 Atom 30 0 Atoms with an Unusual Number of Attached Atoms : Type Atom Name Atom Type Expected Found Valence 1-O 6 0 2 Valence 2-AL 0 0 3 Valence 3-AL 0 0 3 Valence 4-AL 0 0 3 Valence 5-AL 0 0 4 Valence 6-AL 0 0 4 Valence 7-AL 0 0 4 Valence 8-O 6 0 2 Valence 9-O 6 0 2 Valence 10-O 6 0 2 Valence 11-O 6 0 2 Valence 12-O 6 0 2 Valence 13-O 6 0 2 Valence 14-O 6 0 2 Valence 15-O 6 0 2 Valence 16-O 6 0 2 Valence 17-O 6 0 2 Valence 18-O 6 0 2 Valence 19-O 6 0 2 Valence 20-O 6 0 2 Valence 21-O 6 0 2 Valence 22-O 6 0 2 Valence 23-AL 0 0 3 Valence 24-AL 0 0 3 Valence 25-AL 0 0 4 Valence 26-AL 0 0 3 Valence 27-AL 0 0 3 Valence 28-AL 0 0 3 Valence 29-AL 0 0 3 Valence 30-AL 0 0 3 Valence 31-O 6 0 2 Valence 32-O 6 0 2 Valence 33-O 6 0 2 Valence 34-O 6 0 2 Valence 35-O 6 0 2 Valence 36-O 6 0 2 Valence 37-O 6 0 2 Valence 38-O 6 0 2 Valence 40-O 6 0 1 Undefined Out-of-Plane Bending Parameters : Type Atom Names Atom Classes Angle-OP 2-AL 14-O 0 0 Angle-OP 2-AL 13-O 0 0 Angle-OP 2-AL 10-O 0 0 Angle-OP 3-AL 16-O 0 0 Angle-OP 3-AL 15-O 0 0 Angle-OP 3-AL 12-O 0 0 Angle-OP 4-AL 15-O 0 0 Angle-OP 4-AL 11-O 0 0 Angle-OP 4-AL 8-O 0 0 Angle-OP 23-AL 34-O 0 0 Angle-OP 23-AL 22-O 0 0 Angle-OP 23-AL 8-O 0 0 Angle-OP 24-AL 31-O 0 0 Angle-OP 24-AL 17-O 0 0 Angle-OP 24-AL 10-O 0 0 Angle-OP 26-AL 36-O 0 0 Angle-OP 26-AL 33-O 0 0 Angle-OP 26-AL 14-O 0 0 Angle-OP 27-AL 37-O 0 0 Angle-OP 27-AL 34-O 0 0 Angle-OP 27-AL 16-O 0 0 Angle-OP 28-AL 35-O 0 0 Angle-OP 28-AL 33-O 0 0 Angle-OP 28-AL 18-O 0 0 Angle-OP 29-AL 36-O 0 0 Angle-OP 29-AL 31-O 0 0 Angle-OP 29-AL 19-O 0 0 Angle-OP 30-AL 37-O 0 0 Angle-OP 30-AL 32-O 0 0 Angle-OP 30-AL 21-O 0 0 MECHANIC -- Some Required Potential Energy Parameters are Undefined TINKER is Unable to Continue; Terminating the Current Calculation ddikick.exe: application process 0 quit unexpectedly. ddikick.exe: Sending kill signal to DDI processes. ddikick.exe: Execution terminated due to error(s).