From chemistry-request@ccl.net Thu May 22 00:15:56 2003 Received: from marcy.nas.nasa.gov (marcy.nas.nasa.gov [129.99.113.17]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4M4Ftbc024833 for ; Thu, 22 May 2003 00:15:56 -0400 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.7+Sun/8.11.6/NAS 8.11.6-5n) with ESMTP id h4M4Fic09656; Wed, 21 May 2003 21:15:44 -0700 (PDT) Date: Wed, 21 May 2003 21:15:44 -0700 (PDT) From: Ioana Cozmuta To: ancarauta cc: jkl(at)ccl.net, CHEMISTRY(at)ccl.net Subject: Re: CCL:periodic system In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Try CRYSTAL/DISPLAY_STYLE "ONE-CELL" (Deck:Builders1/Crystal Builder/Build Crystal-Preferences/One-Cell Visualisation Style Hope this solves your problem. Ioana On Wed, 21 May 2003, ancarauta wrote: > Hi. > > I'm calculating a periodic system but the solvent > > molecules are blowing up the box. Does anybodry help me? > > > > Thanks a lot. > > > > Alexandre Carauta > PS.: I'm using the CERIUS program and the density is ok. > > Thanks a lot in advance. > > Alexandre Carauta > > > --- > UOL, o melhor da Internet > http://www.uol.com.br/ > > > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY(at)ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST(at)ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl(at)ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu May 22 01:17:13 2003 Received: from mail.rnd.lgchem.com ([150.150.103.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4M5HCbc026215 for ; Thu, 22 May 2003 01:17:13 -0400 Subject: CHARMM parameterization method..?? MIME-Version: 1.0 From: "=?euc-kr?B?wMy787/t?=" To: CHEMISTRY*at*ccl.net Message-ID: Date: Thu, 22 May 2003 14:16:49 +0900 X-MIMETrack: Serialize by Router on LGCHEMDJ01/LGChem/LGChemical(Release 5.0.9a |January 7, 2002) at 2003/05/22 02:16:53 PM MIME-Version: 1.0 Content-Type: text/html; charset=EUC-KR Content-Transfer-Encoding: quoted-printable Untitled

 Hi. CCLer

 

I have some questions about CHA= RMM parameterization.

 

Now, i'd like calculate the pol= ymer system. (Non-biology system)

 

But, CHARMM force field does't = support the polymer units.

 

So, i'd like make parameters ab= out polymer units.

 

(Bond, angle, dihedral force co= nstant, and non-bond interaction parameters.)

 

Just, i only know that these va= lues can be calculated by ab initio program such as=20 GAUSSIAN98.

 

However, i can't use the GAUSSI= AN output.

 

How the force constant matrix c= an be converted to the bond, angle... force constants.

 

 

Anyone who know the proceduer o= f parameterization.

 

Please let me know about it...<= /p>

 

Thank you.

 

Best regard.

 

 

~~~~~~~~~~~~~~~~~~~~~~~~~~~
Lee Sang Uck
Research Scientist 
Computational Chemistry, Coporate R&D
TEL : 042-866-2793
FAX : 042-863-7466
HOME : http://my.netian.com/~deugi
~~~~~~~~~~~~~~~~~~~~~~~~~~~ 

 

= From chemistry-request@ccl.net Thu May 22 08:46:06 2003 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4MCk4bc005050 for ; Thu, 22 May 2003 08:46:06 -0400 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Thu, 22 May 2003 09:48:35 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56B36:at:correio.cetem.gov.br> From: Ian Hovell To: =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= Subject: CCL:Summary Scipcm job fails to complete Date: Thu, 22 May 2003 09:48:29 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Many thanks to all those who replied to the above problem. The replies I have received are listed below. Ian Hovell e-mail: hovell:at:cetem.gov.br Ian Hovell wrote: > > Dear CCLers, > Below is an edited output from a failed gaussian job. > It fails stating: ShPair-CalcS2-2 allocation failure: > I have been unable to find any reference to this in the manual. > Can any body shed any light on this problem > TIA > Ian > %mem MW > %nproc=1 > Will use up to 1 processors via shared memory. > Default route: MaxDisk 00MB > ------------------------------------------ > # rhf/3-21g* scrf=scipcm geom=connectivity > ------------------------------------------ > 1/38=1,57=2/1; > 2/17=6,18=5,40=1/2; > 3/5=5,7=1,11=1,25=1,30=1/1,2,3; > 4/7=1/1; > 5/5=2,32=1,38=4,40 00/2; > 6/7=2,8=2,9=2,10=2,28=1/1; > 99/5=1,9=1/99; > ----------------------------------- > Solvated Solutes: hydroxyquinaldine > ----------------------------------- > Symbolic Z-matrix: > Charge = 0 Multiplicity = 1 > C > C 1 1.3604 > C 2 1.42079 1 119.7042 > C 3 1.40232 2 118.70315 1 0.34555 0 > C 4 1.41382 3 120.51752 2 -0.18059 0 > C 5 1.35698 4 119.39375 3 0.01308 0 > H 1 1.07087 2 119.8106 3 179.80729 0 > N 3 1.36706 2 119.24129 1 -179.8798 0 > C 4 1.42029 3 117.18863 2 179.53833 0 > H 5 1.07213 4 119.27995 3 179.97652 0 > H 6 1.07187 5 120.4652 4 -179.87495 0 > C 9 1.351 4 119.63294 3 -0.08886 0 > C 8 1.30384 3 119.65922 2 -179.2798 0 > H 9 1.07275 4 119.13639 3 -179.92619 0 > H 12 1.07142 9 121.24498 4 -179.79238 0 > O 2 1.36814 1 123.62778 6 179.62457 0 > H 16 0.96618 2 113.32298 1 -0.66918 0 > C 13 1.51008 8 120.08982 3 179.47196 0 > H 18 1.08504 13 110.04764 8 -121.81192 0 > H 18 1.07866 13 110.46305 8 -1.29531 0 > H 18 1.08544 13 110.22502 8 119.45484 0 > ---------------------------Cut out put---------------------------- > Projected INDO Guess. > Warning! Cutoffs for single-point calculations used. > Requested convergence on RMS density matrix=1.00D-04 within 64 cycles. > Requested convergence on MAX density matrix=1.00D-02. > Requested convergence on energy=5.00D-05. > ShPair-CalcS2-2 allocation failure: iend,mxcore= 166464 137127 > Error termination via Lnk1e in C:\G98W\l502.exe. > Job cpu time: 0 days 0 hours 13 minutes 28.0 seconds. > File lengths (MBytes): RWF= 14 Int= 0 D2E= 0 Chk= 1 Scr= 1 > Replies: Dr. Hovell, Any time you see a message from Gaussian concerning "allocation" it is related to insufficient memory. The value for iend is the amount of memory needed at this point and MxCore the amount available. This can often be a second or third allocation from the total specified in %mem so what you need is to increase memory by at least the difference. In your case, > ShPair-CalcS2-2 allocation failure: iend,mxcore= 166464 137127 the available memory is insufficient by only about 30000 words. You could try to sneak this through by adding just that much but unless you are very close to the physical memory on your system I would recommend allocating a bit more so %mem mw will almost certainly work. If you are running short on memory then %mem 290kw would increase it by 50KW. (10*1024KW + 50KW) Most probably it is due to low memory, please increase %mem mw and try again. Best, Yixuan Wang Dept. Chem. Eng. Univ. SC As it is written, you have a memory allocation failure. So increase the memory: %MEM MW should be enough in this case. Nicolas You seem to be short on allocated memory try a line such as %MEM 0MB or whatever you can spare in your com file at the top and see if the job gets further. All the best Laurence Cuffe Looks like you don't have enough memory. Try increasing your %mem assignment and see if that helps. (10MW is 80MB by the way, so you likely can increase this on a newer PC.) John On inspecting the molecule, it is a planar aromatic ring system in the x-y plane, thus most starting atoms has a very small z value (< 0.01). On the other hand, the numbering of Z matrix is quite jumbled. Try to construct a new one with slightly rotated molecule. Dr. Tamas E. Gunda University of Debrecen Medical and Health Science Center Dept. of Pharmaceutical Chemistry POBox 36 H-4010 Debrecen Hungary e-mail: tamasgunda*AT*tigris.klte.hu From chemistry-request@ccl.net Thu May 22 08:46:02 2003 Received: from Post-Office.UH.EDU (NS3.UH.EDU [129.7.1.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4MCk2bc005038 for ; Thu, 22 May 2003 08:46:02 -0400 Received: from nyssa.bchs.uh.edu (Nyssa.BCHS.UH.EDU [129.7.238.204]) by Post-Office.UH.EDU (PMDF V6.0-025 #30599) with ESMTP id <0HFA02IOJGSJHB=at=Post-Office.UH.EDU> for CHEMISTRY=at=ccl.net; Thu, 22 May 2003 07:45:55 -0500 (CDT) Date: Thu, 22 May 2003 07:43:26 -0700 From: Jerry Ebalunode Subject: CCL:re:shifting coordinates with CHARMM In-reply-to: <200305220929.35135.hloeffler=at=lac.chem.nagoya-u.ac.jp> To: Hannes Loeffler Cc: CHEMISTRY=at=ccl.net Reply-to: jebalunode=at=adrik.bchs.uh.edu Message-id: <200305220743.26879.jebalunode=at=adrik.bchs.uh.edu> Organization: University of Houston MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit Content-disposition: inline User-Agent: KMail/1.5.2 References: <200305220929.35135.hloeffler=at=lac.chem.nagoya-u.ac.jp> You can recenter the coordinates to align with the axis by adding this charmm command lines before the instructions for writing out the the translated molecule to an output file . Hope this helps. coor orient sele all end define origin select all end coordinate statistics coor translate xdirection -?XAVE ydirection -?YAVE zdirection -?ZAVE On Wednesday 21 May 2003 05:29 pm, you wrote: > Hi, > > is it possible to re-center coordinates with CHARMM? Some viewing programs > are not aware of PBCs and during a simulation the system of interest may > diffuse to the edges of the box. It might be useful, therefore, to shift > an atom (or maybe an arbritary point in space) to the center of the box. > > TIA, > Hannes. > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line and send your message to: CHEMISTRY=at=ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST=at=ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl=at=ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Jerry Ebalunode Graduate Research Assistant RM 402F Houston Science Center Dept. of Biology and Biochemistry University of Houston. 4800 Calhoun Road Houston, TX 77204 From chemistry-request@ccl.net Thu May 22 05:18:58 2003 Received: from mehl.gfz-potsdam.de (mehl.gfz-potsdam.de [139.17.1.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4M9Ivbc032345 for ; Thu, 22 May 2003 05:18:57 -0400 Received: from fwng.gfz-potsdam.de (virscan [139.17.1.10]) by mehl.gfz-potsdam.de (8.12.9/8.12.9) with SMTP id h4M9IusE014232 for ; Thu, 22 May 2003 11:18:56 +0200 (MET DST) Date: Thu, 22 May 2003 11:18:54 +0200 Mime-Version: 1.0 (Apple Message framework v552) Content-Type: multipart/alternative; boundary=Apple-Mail-6-126007010 Subject: CCL:PBC calculation fails to complete with g03 From: Matthias Gottschalk To: CHEMISTRY=at=ccl.net Message-Id: <68E31992-8C36-11D7-BB64-00039319731C=at=gfz-potsdam.de> X-Mailer: Apple Mail (2.552) --Apple-Mail-6-126007010 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Hello, I try to to make a simple PBC calculation for diamond, but the job fails to complete. Because documentation in respect to the new PBC feature in g03 seems to be very scarce, I can not figure out what I am doing wrong. The com file looks like this: %chk=output %mem=512MB %nproc=1 # rhf/6-31g(d) test Diamond 0 1 C 0.44500000 0.44500000 0.44500000 C 1.33500000 1.33500000 1.33500000 C 0.44500000 2.22500000 2.22500000 C 3.11500000 1.33500000 3.11500000 C 2.22500000 0.44500000 2.22500000 C 1.33500000 3.11500000 3.11500000 C 2.22500000 2.22500000 0.44500000 C 3.11500000 3.11500000 1.33500000 Tv 3.56000000 0.00000000 0.00000000 Tv 0.00000000 3.56000000 0.00000000 Tv 0.00000000 0.00000000 3.56000000 The log file is essentially this (possible clues are bold): ****************************************** Gaussian 03: MacOSX-G03RevB.03 4-May-2003 22-May-2003 ****************************************** %chk=output %mem=512MB %nproc=1 Will use up to 1 processors via shared memory. -------------------------- # rhf/6-31g(d) scf=qc test -------------------------- 1/38=1/1; 2/17=6,18=5,40=1/2; 3/5=1,6=6,7=1,11=1,16=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,8=3,32=1,38=5/8; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; ------- Diamond ------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C 0.445 0.445 0.445 C 1.335 1.335 1.335 C 0.445 2.225 2.225 C 3.115 1.335 3.115 C 2.225 0.445 2.225 C 1.335 3.115 3.115 C 2.225 2.225 0.445 C 3.115 3.115 1.335 Tv 3.56 0. 0. Tv 0. 3.56 0. Tv 0. 0. 3.56 Before rotation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 .445000 .445000 .445000 2 6 0 1.335000 1.335000 1.335000 3 6 0 .445000 2.225000 2.225000 4 6 0 3.115000 1.335000 3.115000 5 6 0 2.225000 .445000 2.225000 6 6 0 1.335000 3.115000 3.115000 7 6 0 2.225000 2.225000 .445000 8 6 0 3.115000 3.115000 1.335000 9 -2 0 3.560000 .000000 .000000 10 -2 0 .000000 3.560000 .000000 11 -2 0 .000000 .000000 3.560000 --------------------------------------------------------------------- Lengths of translation vectors: 3.560000 3.560000 3.560000 Angles of translation vectors: 90.000000 90.000000 90.000000 --------------------------------------------------------------------- Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 -1.335000 -1.335000 -1.335000 2 6 0 -.445000 -.445000 -.445000 3 6 0 -1.335000 .445000 .445000 4 6 0 1.335000 -.445000 1.335000 5 6 0 .445000 -1.335000 .445000 6 6 0 -.445000 1.335000 1.335000 7 6 0 .445000 .445000 -1.335000 8 6 0 1.335000 1.335000 -.445000 9 -2 0 3.560000 .000000 .000000 10 -2 0 .000000 3.560000 .000000 11 -2 0 .000000 .000000 3.560000 --------------------------------------------------------------------- Lengths of translation vectors: 3.560000 3.560000 3.560000 Angles of translation vectors: 90.000000 90.000000 90.000000 --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 C .000000 2 C 1.541525 .000000 3 C 2.517300 1.541525 .000000 4 C 3.879420 2.517300 2.951796 .000000 5 C 2.517300 1.541525 2.517300 1.541525 .000000 6 C 3.879420 2.517300 1.541525 2.517300 2.951796 7 C 2.517300 1.541525 2.517300 2.951796 2.517300 8 C 3.879420 2.517300 2.951796 2.517300 2.951796 9 TV 5.246473 4.054143 4.935289 2.632656 3.418110 10 TV 5.246473 4.054143 3.418110 4.427694 4.935289 11 TV 5.246473 4.054143 3.418110 2.632656 3.418110 6 7 8 9 10 6 C .000000 7 C 2.951796 .000000 8 C 2.517300 1.541525 .000000 9 TV 4.427694 3.418110 2.632656 .000000 10 TV 2.632656 3.418110 2.632656 5.034600 .000000 11 TV 2.632656 4.935289 4.427694 5.034600 5.034600 11 11 TV .000000 Symmetry turned off: Cannot cope with ghost atoms or with translation vectors. Stoichiometry C8 Framework group C1[X(C8)] Deg. of freedom 18 Full point group C1 NOp 1 Standard basis: 6-31G(d) (6D, 7F) Integral buffers will be 262144 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned off. 120 basis functions, 224 primitive gaussians, 120 cartesian basis functions 24 alpha electrons 24 beta electrons nuclear repulsion energy 230.7751807790 Hartrees. NAtoms= 8 NActive= 8 NUniq= 8 SFac= 1.00E+00 NAtFMM= 60 Big=F FOutLm= 100.00. Periodicity: 1 1 1 Max integer dimensions: 15 15 15 PBC vector 1 X= 6.7274 Y= .0000 Z= .0000 PBC vector 2 X= .0000 Y= 6.7274 Z= .0000 PBC vector 3 X= .0000 Y= .0000 Z= 6.7274 Recp vector 1 X= .1486 Y= .0000 Z= .0000 Recp vector 2 X= .0000 Y= .1486 Z= .0000 Recp vector 3 X= .0000 Y= .0000 Z= .1486 Generated k point mesh (from -Pi to Pi): K space mesh: X= 34 Y= 34 Z= 34 A half-cell shift: 1 Using k point mesh (from -Pi to Pi): K space mesh: X= 34 Y= 34 Z= 34 A half-cell shift: 1 CountK=T Total number of k points: 0 CountK=T Total number of k points: 19652 STVDrv-2 allocation failure: iend,mxcore= 269166433 67108864 Error termination via Lnk1e in /Applications/g03/l302.exe at Thu May 22 10:55:26 2003. Job cpu time: 0 days 0 hours 1 minutes 30.3 seconds. File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 7 Scr= 1 Can anybody help me? Sincerely Matthias -- PD Dr. Matthias Gottschalk GeoForschungsZentrum Projektbereich 4.1 Telegrafenberg 14473 Potsdam Germany tel/fax +49 (0) 331 288-1418/1402 --Apple-Mail-6-126007010 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Hello, I try to to make a simple PBC calculation for diamond, but the job fails to complete. Because documentation in respect to the new PBC feature in g03 seems to be very scarce, I can not figure out what I am doing wrong. The com file looks like this: %chk=output %mem=512MB %nproc=1 # rhf/6-31g(d) test Diamond 0 1 C 0.44500000 0.44500000 0.44500000 C 1.33500000 1.33500000 1.33500000 C 0.44500000 2.22500000 2.22500000 C 3.11500000 1.33500000 3.11500000 C 2.22500000 0.44500000 2.22500000 C 1.33500000 3.11500000 3.11500000 C 2.22500000 2.22500000 0.44500000 C 3.11500000 3.11500000 1.33500000 Tv 3.56000000 0.00000000 0.00000000 Tv 0.00000000 3.56000000 0.00000000 Tv 0.00000000 0.00000000 3.56000000 The log file is essentially this (possible clues are bold): ****************************************** Gaussian 03: MacOSX-G03RevB.03 4-May-2003 22-May-2003 ****************************************** %chk=output %mem=512MB %nproc=1 Will use up to 1 processors via shared memory. -------------------------- # rhf/6-31g(d) scf=qc test -------------------------- 1/38=1/1; 2/17=6,18=5,40=1/2; 3/5=1,6=6,7=1,11=1,16=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,8=3,32=1,38=5/8; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; ------- Diamond ------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C 0.445 0.445 0.445 C 1.335 1.335 1.335 C 0.445 2.225 2.225 C 3.115 1.335 3.115 C 2.225 0.445 2.225 C 1.335 3.115 3.115 C 2.225 2.225 0.445 C 3.115 3.115 1.335 Tv 3.56 0. 0. Tv 0. 3.56 0. Tv 0. 0. 3.56 Before rotation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 .445000 .445000 .445000 2 6 0 1.335000 1.335000 1.335000 3 6 0 .445000 2.225000 2.225000 4 6 0 3.115000 1.335000 3.115000 5 6 0 2.225000 .445000 2.225000 6 6 0 1.335000 3.115000 3.115000 7 6 0 2.225000 2.225000 .445000 8 6 0 3.115000 3.115000 1.335000 9 -2 0 3.560000 .000000 .000000 10 -2 0 .000000 3.560000 .000000 11 -2 0 .000000 .000000 3.560000 --------------------------------------------------------------------- Lengths of translation vectors: 3.560000 3.560000 3.560000 Angles of translation vectors: 90.000000 90.000000 90.000000 --------------------------------------------------------------------- Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 -1.335000 -1.335000 -1.335000 2 6 0 -.445000 -.445000 -.445000 3 6 0 -1.335000 .445000 .445000 4 6 0 1.335000 -.445000 1.335000 5 6 0 .445000 -1.335000 .445000 6 6 0 -.445000 1.335000 1.335000 7 6 0 .445000 .445000 -1.335000 8 6 0 1.335000 1.335000 -.445000 9 -2 0 3.560000 .000000 .000000 10 -2 0 .000000 3.560000 .000000 11 -2 0 .000000 .000000 3.560000 --------------------------------------------------------------------- Lengths of translation vectors: 3.560000 3.560000 3.560000 Angles of translation vectors: 90.000000 90.000000 90.000000 --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 C .000000 2 C 1.541525 .000000 3 C 2.517300 1.541525 .000000 4 C 3.879420 2.517300 2.951796 .000000 5 C 2.517300 1.541525 2.517300 1.541525 .000000 6 C 3.879420 2.517300 1.541525 2.517300 2.951796 7 C 2.517300 1.541525 2.517300 2.951796 2.517300 8 C 3.879420 2.517300 2.951796 2.517300 2.951796 9 TV 5.246473 4.054143 4.935289 2.632656 3.418110 10 TV 5.246473 4.054143 3.418110 4.427694 4.935289 11 TV 5.246473 4.054143 3.418110 2.632656 3.418110 6 7 8 9 10 6 C .000000 7 C 2.951796 .000000 8 C 2.517300 1.541525 .000000 9 TV 4.427694 3.418110 2.632656 .000000 10 TV 2.632656 3.418110 2.632656 5.034600 .000000 11 TV 2.632656 4.935289 4.427694 5.034600 5.034600 11 11 TV .000000 Symmetry turned off: Cannot cope with ghost atoms or with translation vectors. Stoichiometry C8 Framework group C1[X(C8)] Deg. of freedom 18 Full point group C1 NOp 1 Standard basis: 6-31G(d) (6D, 7F) Integral buffers will be 262144 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned off. 120 basis functions, 224 primitive gaussians, 120 cartesian basis functions 24 alpha electrons 24 beta electrons nuclear repulsion energy 230.7751807790 Hartrees. NAtoms= 8 NActive= 8 NUniq= 8 SFac= 1.00E+00 NAtFMM= 60 Big=F FOutLm= 100.00. Periodicity: 1 1 1 Max integer dimensions: 15 15 15 PBC vector 1 X= 6.7274 Y= .0000 Z= .0000 PBC vector 2 X= .0000 Y= 6.7274 Z= .0000 PBC vector 3 X= .0000 Y= .0000 Z= 6.7274 Recp vector 1 X= .1486 Y= .0000 Z= .0000 Recp vector 2 X= .0000 Y= .1486 Z= .0000 Recp vector 3 X= .0000 Y= .0000 Z= .1486 Generated k point mesh (from -Pi to Pi): K space mesh: X= 34 Y= 34 Z= 34 A half-cell shift: 1 Using k point mesh (from -Pi to Pi): K space mesh: X= 34 Y= 34 Z= 34 A half-cell shift: 1 CountK=T Total number of k points: 0 CountK=T Total number of k points: 19652 STVDrv-2 allocation failure: iend,mxcore= 269166433 67108864 Error termination via Lnk1e in /Applications/g03/l302.exe at Thu May 22 10:55:26 2003. Job cpu time: 0 days 0 hours 1 minutes 30.3 seconds. File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 7 Scr= 1 Can anybody help me? Sincerely Matthias -- PD Dr. Matthias Gottschalk GeoForschungsZentrum Projektbereich 4.1 Telegrafenberg 14473 Potsdam Germany tel/fax +49 (0) 331 288-1418/1402 --Apple-Mail-6-126007010-- From chemistry-request@ccl.net Thu May 22 09:58:33 2003 Received: from polaris.scs.uiuc.edu (polaris.scs.uiuc.edu [130.126.225.41]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4MDwXbc007382 for ; Thu, 22 May 2003 09:58:33 -0400 Received: from leonidas (leonidas.scs.uiuc.edu [130.126.226.239]) by polaris.scs.uiuc.edu (8.12.9/8.12.8) with SMTP id h4MDwWED5209595; Thu, 22 May 2003 08:58:32 -0500 (CDT) Reply-To: From: "Jerome Baudry" To: "'ancarauta'" , Cc: Subject: RE: periodic system Date: Thu, 22 May 2003 08:55:13 -0500 Message-ID: <000801c32069$c5355ed0$efe27e82@leonidas> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2911.0) In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal Do you mean the unit cell's dimensions increase during a minimization? Or a MD simulation? What you want to keep fixed depends on what your experimental variable is: if you know that the density is OK, but you came up with an initial guess for the cell's volume, then I see nothing wrong in changing the cell's dimensions to reproduce the correct density. If you are using a know crystal structure, then indeed the cell's dimensions should be kept. THis being said, does the crystal structure includes solvent? if no, you may have added to much solvent, or added solvent molecules so close to the solute that the intial forces 'explodes' the system. You might first want to keep the unit cell' dimensions fixed during an initial minimization step: OFF METHODS >> MINIMIZER >> CONSTRAINTS >> CELL then uncheck the a,b,c dimensions, so that the unit cell's volume will be constant (not done by default). ---------------------------------------------------------- Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. School of Chemical Sciences University of Illinois at Urbana-Champaign 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: jerome*at*scs.uiuc.edu > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request*at*ccl.net]On > Behalf Of ancarauta > Sent: Wednesday, May 21, 2003 4:53 PM > To: jkl*at*ccl.net > Cc: CHEMISTRY*at*ccl.net > Subject: CCL:periodic system > > > Hi. > > I'm calculating a periodic system but the solvent > > molecules are blowing up the box. Does anybodry help me? > > > > Thanks a lot. > > > > Alexandre Carauta > PS.: I'm using the CERIUS program and the density is ok. > > Thanks a lot in advance. > > Alexandre Carauta > > > --- > UOL, o melhor da Internet > http://www.uol.com.br/ > > > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on > your Subject: line > and send your message to: CHEMISTRY*at*ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST*at*ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the > maintainer: > Jan Labanowski, jkl*at*ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > From chemistry-request@ccl.net Thu May 22 11:37:35 2003 Received: from kafka.net.nih.gov (kafka.net.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4MFbYbc010651 for ; Thu, 22 May 2003 11:37:34 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.9/8.12.9) with ESMTP id h4MFbFx9021447; Thu, 22 May 2003 11:37:15 -0400 (EDT) Date: Thu, 22 May 2003 11:09:39 -0400 From: Rick Venable To: Jerry Ebalunode cc: Hannes Loeffler , CHEMISTRY[at]ccl.net Subject: Re: CCL:re:shifting coordinates with CHARMM In-Reply-To: <200305220743.26879.jebalunode[at]adrik.bchs.uh.edu> Message-ID: References: <200305220929.35135.hloeffler[at]lac.chem.nagoya-u.ac.jp> <200305220743.26879.jebalunode[at]adrik.bchs.uh.edu> ReplyTo: Rick_Venable[at]nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII That's not quite correct-- a solvated box would be rotated to be align a diagonal with the X axis by the COOR ORIENT command in the reply below; you must use NOROT to supress rotation. An image update is also needed to re-pack the solvent (and possibly ions) once the macromolecule has been moved to the Cartesian origin. To move the solute and repack the solvent, etc., images must be present (IMAGE or CRYSTAL) and image centering setup for solvent etc. via IMAGE BYRES; then COOR ORIENT NOROT SELE SEGID A END ! move segid A to origin UPDATE IMGFRQ 1 ! force an image update On Thu, 22 May 2003, Jerry Ebalunode wrote: > You can recenter the coordinates to align with the axis by adding this > charmm command lines before the instructions for writing out the the > translated molecule to an output file . Hope this helps. > > > coor orient sele all end > define origin select all end > coordinate statistics > coor translate xdirection -?XAVE ydirection -?YAVE zdirection -?ZAVE > On Wednesday 21 May 2003 05:29 pm, Hannes Loeffler wrote: > > is it possible to re-center coordinates with CHARMM? Some viewing > > programs are not aware of PBCs and during a simulation the system of > > interest may diffuse to the edges of the box. It might be useful, > > therefore, to shift an atom (or maybe an arbritary point in space) > > to the center of the box. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable[at]nih.gov ALT email: rvenable[at]speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Thu May 22 11:24:02 2003 Received: from kafka.net.nih.gov (mailfwd.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4MFO1bc010215 for ; Thu, 22 May 2003 11:24:02 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.9/8.12.9) with ESMTP id h4MFO0x9020243; Thu, 22 May 2003 11:24:00 -0400 (EDT) Date: Thu, 22 May 2003 10:56:23 -0400 From: Rick Venable To: =?euc-kr?B?wMy787/t?= cc: CHEMISTRY.-at-.ccl.net Subject: CCL: Re: CHARMM parameterization method..?? In-Reply-To: Message-ID: References: ReplyTo: Rick_Venable.-at-.nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=EUC-KR Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h4MFO2bc010217 On Thu, 22 May 2003, [euc-kr] @L;s?m wrote: > I have some questions about CHARMM parameterization. > > Now, i'd like calculate the polymer system. (Non-biology system) > > But, CHARMM force field does't support the polymer units. > > So, i'd like make parameters about polymer units. > > (Bond, angle, dihedral force constant, and non-bond interaction > parameters.) > > Just, i only know that these values can be calculated by ab initio > program such as GAUSSIAN98. See the info and references at URL http://www.pharmacy.umaryland.edu/~alex/research.html Bond and angle force constants are derived from IR/Raman spectroscopy wherever possible; ab initio calcs are used to refine torsional energy terms, and for initial partial charges. Partial charges and VDW parameters are adjusted iteratively based on thermodynamic properties > from MC or MD calculations, including interactions with the TIP3 water model. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable.-at-.nih.gov ALT email: rvenable.-at-.speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Thu May 22 12:49:17 2003 Received: from bilbo.fq.edu.uy (bilbo.fq.edu.uy [164.73.160.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4MGnEbc012831 for ; Thu, 22 May 2003 12:49:16 -0400 Received: from Inorganica03 (Inorganica03.fq.edu.uy [164.73.160.179]) by bilbo.fq.edu.uy (8.12.1/8.12.1) with SMTP id h4MGn4g5005863 for ; Thu, 22 May 2003 13:49:04 -0300 Message-ID: <00d901c32082$abfe1a60$b3a049a4$at$fq.edu.uy> From: "Jorge S. Gancheff" To: Subject: PCM cavity problems Date: Thu, 22 May 2003 13:53:28 -0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00D6_01C32069.860909A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 This is a multi-part message in MIME format. ------=_NextPart_000_00D6_01C32069.860909A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, I=B4m working with some Re(V) complexes using DFT in aqueous solution = (Gaussian 98, Rev. A11). I=B4m using the PCM method to simulate the = presence of the solvent. Although I have using this method succesfully, = when the system include explicit water molecules, in some cases, the = calculation aborted giving the following message: Cycle 1 Pass 1 IDiag 1: TESSERA: too many vertices in a tessera Error termination via Lnk1e in = /usr/local/fbscapp/g98_A.11.3/g98/l502.exe. Job cpu time: 0 days 1 hours 3 minutes 56.9 seconds. File lengths (MBytes): RWF=3D 94 Int=3D 0 D2E=3D 0 Chk=3D 2 = Scr=3D 1 The problem seems to be independent of the cavity geometry. =20 I`m using several cavity: from PENTAKISDODECAHEDRA (with 60 initial = tesserae, by default) to TETRAHEDRA (with 4 initial tesserae).=20 =20 Can anybody help me? Sincerely, =20 Jorge=20 =20 M.Sc. Jorge S. Gancheff jorge$at$bilbo.edu.uy =20 ------=_NextPart_000_00D6_01C32069.860909A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello,
 
I=B4m working with some Re(V) = complexes using=20 DFT in aqueous solution (Gaussian 98, Rev. A11). I=B4m using the PCM = method to=20 simulate the presence of the solvent. Although I have using this method=20 succesfully, when the system include explicit water molecules, in = some=20 cases, the calculation aborted giving the following = message:
 
Cycle   1  Pass 1  = IDiag=20 1:
  TESSERA: too many vertices in a = tessera
 Error=20 termination via Lnk1e in=20 /usr/local/fbscapp/g98_A.11.3/g98/l502.exe.
 Job cpu=20 time:  0 days  1 hours  3 minutes 56.9 = seconds.
 File=20 lengths (MBytes):  RWF=3D   94 Int=3D    0 = D2E=3D    0 Chk=3D    2 = Scr=3D   =20 1
 
The problem seems to = be independent of the=20 cavity geometry.
 
I`m using several cavity:=20 from PENTAKISDODECAHEDRA (with  60 initial tesserae, by = default) to=20 TETRAHEDRA (with 4 initial tesserae).
 
Can anybody help me?
 
Sincerely,
 
Jorge
 
M.Sc. Jorge S. Gancheff
jorge$at$bilbo.edu.uy
 
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