From chemistry-request@server.ccl.net Tue Feb 26 09:23:30 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1QENU522090 for ; Tue, 26 Feb 2002 09:23:30 -0500 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA02715 for ; Tue, 26 Feb 2002 09:23:04 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3C7B9A48.C2E4A7F2@cornell.edu> Date: Tue, 26 Feb 2002 09:23:04 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 CC: "'chemistry@ccl.net'" Subject: Re: CCL: Hydrophobic ligands (was molecular docking startup) References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Interesting. Anyone else have comments on docking hydrophobic ligands? Right away I can think of a couple reasons why hydrophobics would be difficult. Without strong, directed polar interactions, the binding site would naturally be shallower and less well defined. Docking programs without a good solvent model may also contribute to the problem, but I wonder if that is really a significant factor or not. There was a paper just out in J. Comp. Chem. about the failure of point charge models to correctly reproduce crystal lattices of n-alkanes: "On the irrelevance of electrostatics for the crystal structures and polymorphism of long even n-alkanes" Jacco Van de Streek, Paul Verwer, Piet Bennema, Elias Vlieg (JCP v23 #3 2002) Anyone worked with the Thermal Motion Forcefield (TMFF) mentioned in the article, or know where the paper is supposed to come out? Richard Gillilan MacCHESS > Stewart Kirton wrote: > .... > recommend that you start here. However, it has limitations - and if you > are looking to dock largely hydrophobic ligands into hydrophobic > structures it probably will frustrate you......saying that so will a lot > of the other packages out there. > From chemistry-request@server.ccl.net Tue Feb 26 09:54:29 2002 Received: from gwia.kvl.dk ([130.225.43.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1QEsS522617 for ; Tue, 26 Feb 2002 09:54:28 -0500 Received: from kvl.dk (pwt.kemi.kvl.dk [130.225.43.124]) by gwia.kvl.dk; Tue, 26 Feb 2002 15:50:41 +0100 Sender: pwt@ccl.net Message-ID: <3C7BA287.C6DA976D@kvl.dk> Date: Tue, 26 Feb 2002 15:58:15 +0100 From: Peter Waaben Thulstrup Organization: Royal Veterinary and Agricultural University X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.10-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: G98: How to extract force constants from output? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL Can anybody give simple instructions on extracting stretching and bending force constants for individual bonds from G98 output. I hope to compare the computed values to force field parameters. Also, if someone can recommend any key references or monographs on the subject of adapting computed force constants for use in force fields I will be most grateful for the help. Thank you in advance, Peter W. Thulstrup Chemistry Department / Royal Veterinary and Agricultural University Thorvaldsensvej 40 / DK-1871 Frederiksberg C / Denmark Phone: +45 35282464 / Fax: +45 35282398 / E-mail: pwt@kvl.dk From chemistry-request@server.ccl.net Tue Feb 26 09:45:58 2002 Received: from coyote.iupui.edu ([134.68.220.82]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1QEjw522413 for ; Tue, 26 Feb 2002 09:45:58 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by coyote.iupui.edu (8.9.3/8.9.3/IUPUIPO.20020221) with SMTP id JAA24986; Tue, 26 Feb 2002 09:45:17 -0500 (EST) Message-ID: Date: 26 Feb 2002 09:51:51 -0500 From: "Boyd" Subject: Emerging Technologies Prize To: "CHMINF-L" , "MEDI ACS Listserv" , "Mol-diversity list" , "OSC CCL" , "PDB list" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Dear Computational Chemists, You are invited to submit an abstract for the 2002 Symposium on Emerging Computational Technologies at the American Chemical Society (ACS) National Meeting, Boston, Massachusetts, USA, August 18-22, 2002. A $1000 prize, kindly sponsored by Schrodinger, Inc., will be presented for the best talk at the symposium. To apply for the competition, please e-mail a long (1000-word, text-only) abstract to me by March 18, 2002. Talks must be original and not be repeats of talks at other ACS symposia. The objective of this COMP symposium is to stimulate, reward, and publicize important methodological advances in computational chemistry. The symposium is ideal for presenting your latest and best research on new techniques and software development. Past winners of the annual $1000 prize: 2000 Dr. Amiram Goldblum, Hebrew University of Jerusalem, Israel 2001 Dr. Christopher Keefer, GlaxoSmithKline, North Carolina More information is available at http://membership.acs.org/C/COMP/ Thanks, Don Prof. Donald B. Boyd Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Department of Chemistry Indiana University-Purdue University at Indianapolis E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Tue Feb 26 06:38:39 2002 Received: from orionl0.ccf.auth.gr ([155.207.199.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1QBcc519299 for ; Tue, 26 Feb 2002 06:38:38 -0500 Received: from chem011 (chem011.chem.auth.gr [155.207.64.94]) by orionl0.ccf.auth.gr (8.11.6/8.11.4/8.11.4) with SMTP id g1QBcAm16866 for ; Tue, 26 Feb 2002 13:38:10 +0200 (EET) Organization: Message-ID: <00a301c1beb9$a99e36f0$5e40cf9b@chem.auth.gr> From: "temper" To: Subject: Summary: MP2 opt Date: Tue, 26 Feb 2002 13:35:15 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00A0_01C1BECA.6C6A94C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-Virus-Scanned: by mail.auth.gr, virus data file v4187 created Feb 20 2002 This is a multi-part message in MIME format. ------=_NextPart_000_00A0_01C1BECA.6C6A94C0 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable Thanks to all, for yours comments. My question was: I've been trying to do a geometry optimization using MP2/6-311++(d,p) = (210 basis functions) with GAUSSIAN 98W A.11 but I can't. WHY?(I have an ATHLON 1.6+GHz with 512 MB memory and 30+ GB hard disk). The operating system is WINDOWS 2000. I defined memory and hard disk: %m=3D180MB ------------------------------------------------- #p mp2/6-311++(d,p) opt scf=3Ddirect maxdisk=3D7000MB ------------------------------------------------- The error from the output is shown below: (Enter C:\G98W\l906.exe) Frozen-core derivative calculation, NFC=3D 10 NFV=3D 0. FulOut=3DF Deriv=3DT AODrv=3DT MMem=3D 3 MDisk=3D 18 MDiskD=3D 18 W3Min=3D 1270080 MinDsk=3D 1759100 NBas6D=3D 216 NBas2D=3D 23697 NTT=3D 23436 LenExt=3D 21464976 MDV=3D 23464976 MDiskM=3D 1380 NBas2p=3D 23300 Disk-based method using ON**2 memory for 18 occupieds at a time. Estimated scratch disk usage=3D 333638376 words. IMap=3D 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 IMap=3D 21 22 23 24 25 26 27 28 Actual scratch disk usage=3D 333205784 words. JobTyp=3D1 Pass 1: I=3D 11 to 28. writwa Can anyone give me an advice? Thanks in advance. All the answers are follow, and thanks again: ***** As far as I know, Windows whatsoever is a 32bit operating system (still some 16 bit stuff around?). Therefore, the size of a single file is = limited to ca. 2 GByte. Beyond that, you have to split your files. This = procedure is described in the handbook. Or have a look at the gaussian website at www.gaussian.com, "Tech info". Regards Wolfgang Roth ***** G98W can only handle scratch files up to 2 GB, although it can use more = than one. From your output, it seems that the MP2 calculation needs = about 2.5 GB. What you have to do is to split the .rwf file into several = (here two) portion (<2GB). See %rwf directive in the G98 help, for = example: %rwf=3Dc:\1.rwf,1.9GB,c:\2.rwf,1.9GB, .... You get the idea? Hope this helps, Rainer Koch. PS: If in doubt, search the CCL archive for more information, this topic = is discussed about every two months or so... ***** the file system of W 20000 does not allow to write large single file u = should separate the .rwf file Just insert the line = %rwf=3Dc:\1\1,2000mb,c:\2\2,2000mb,c:\3\3,2000mb,c:\4\4,2000mb,c:\5\5,200= 0mb in the beginning of the input. u should first create the required paths c:\1, c:\2 etc Panaghiotis Karamanis ***** G98W is a 32 bit application and as such is limited to 2GB=20 pre file. To exceed this you can specify the RWF as a compound file=20 %rwf=3Da,245mw,b,245mw,c,245mw up to a maximum of 8 files. Then the value for MaxDisk should be set to the sum of these files, MaxDisk=3D735MW in my example. This will give you the best chance of completing this. Cust. Service Doug ***** I suspect that the job is failing because the scratch file (*.rwf) is = exceeding 2GB. Remember, Gaussian98 can use up to 16GB of h-drive space = but Win2000 can only use 2GB files. Try this: %rwf=3Da,240MW,b,240MW,c,240MW,d,240MW, %nosave %m=3D180MB #p mp2/6-311++(d,p) opt scf=3Ddirect maxdisk=3D7000MB Good luck, Phil Matz ***** You ran out of space in your rw file. Windows rw files can only be 2GB. = You need about 3GB. Using the options specified in the G98W manual, you can create multiple = rw files. Use that to make 2, 2GB rw files and the job should get past = your present error OK. Jim Kress ***** Dear Vasilios, Your problem looks identical to one which has been asked and answered many times on the CCL. You need to break up your rwf file into Gaussian-sized chunks. Rather than tell you the answer, I'll tell you how to find the answer, which could have saved you a posting in the first place. Think of this when future problems arise: Go to the CCL web page and search the archives for keyword "writwa", which is the tell-tale part of your error message. You will see there is a simple solution. David Anick MD PhD David.Anick@gte.net ***** it needs more disk space. Increase your maxdisk (check the = DEfault.ROute, too). I dont know about g98W, but in linux you have to = assign diferent file names to use as schratch (eg. = %rwf=3Da,200mw,b,200mw,c,200mw,d,200mw ) take care, Guilherme Dinamica Sonora ***** Hi Vasilios. some operating systems have a filesize limit of 2GB. Try the following: a) MaxDisk=3D2040MB or b) splitting the RWF file into several pieces <2GB e.g. %RWF=3D/scr/a,2040MB,/scr/b,2040MB,/scr/c,2040MB ... good luck. Juan Juan Pablo Senosiain ***** Your disk usage is about 1/3 gigawords, or about 2.33 GB. Although this = is well within the size of your hard disk, it's above the per-file limit of = 2GB that some operating systems have, including Microsoft Windows. =20 There is a work-around. Put the following line under your memory specification: %rwf=3Dr1,240mw,r2,240mw,r3,240mw,r4,-1 This will create files of 240 megawords (1960 MB), each of which is = below the 2GB limit, with the names r1.rwf, r2.rwf, r3.rwf, and r4.rwf. When r1.rwf fills up Gaussian will move to r2.rwf and so on. =20 =20 Hope this helps. --David Shobe Sud-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. ***** Dear Vasilios!=20 Try to use the PC GAMESS! Best regards, Alex Granovsky ***** Dear Vasilios: It seems to be a problem with the scratch disk space. Namely, some = versions of Gaussian (G98W included) are not able to handle the files larger than = 2GB (due to the wrong compiling options). To overcome this you should supply some additional input cards, specifying the locations and sizes of these scratch files. See, please, the beginning of the sample input file: %rwf=3DF:\a,2GB,F:\b,2GB,F:\c,2GB,F:\d,2GB,F:\e,2GB,F:\f,2GB,F:\g,2GB,F:\= h,2GB %nosave %chk=3Dfn13mp3_trans.chk %mem=3D1400MB #N QCISD /6-31+G(d) SCF=3D(MAXCYCLE=3D900) geom=3Dcheck guess=3Dread # POP=3DREG GFINPUT IOP(6/7=3D3) pop=3Dminimal scf=3Ddirect fn13 0,1 In the above example a,b,c,d,e,f,g,h are the file names, 2GB each. The length of this record is limited, as I remember to 76 (or 80) = characters. Until to revision A.7 there is no possibility to specify any additional = %rwf cards, thus to me the scratch disk space is limited to 8X2GB=3D16GB. Another thing is that MP2 jobs are very sensitive to the main memory = amount, thus if you have 500MB of main memory, it's better to set this memory = card about 400MB. Never put it 450MB or more, due to the extensive swapping resulting in a very low perfomance. I hope this will help. Andrus Metsala ***** Dear Vasilios I. Teberekidis The file size for G98 on a 32 bit OS is limited to 8 pieces of about 2Gb size to give totally about 16 Gb. insert the following line as link0 line in your input file: %rwf=3D/path/1,1900mb,/path/2,1900mb,/path/3,1900mb,/path/4,1900mb,/path/= 4,1900mb,/path/5,1900mb,/path/6,1900mb,/path/7,1900mb,path/8,-1 /path/ is the path to a scratch directory - such as /scr/ the rwf file will be split into 1900 mb pieces with the names 1.rwf, 2.rwf ..... good luck Hans-Ullrich Siehl =20 ***** =20 Hi, The writwa at the end of the output mentions that you have run out=20 of scratch disk space. You may try one of two things: (1) split the=20 scratch file into 3-5 partitions, or (2) optimise the geometry at a=20 lower or DFT level, and perform a single point MP2 calculation. Cheers, Balakrishnan Balakrishnan Viswanathan Department of Chemistry Dalhousie University Halifax, Nova Scotia Canada B3H 4J3 (902) 494-7021 bviswan@chem1.chem.dal.ca =20 =20 That's all. Postgraduate (Ph.D) Student Vasilios I. Teberekidis Laboratory of Applied Quantum Chemistry=20 Aristotle University of Thessaloniki (Greece) Tel.:(+30 31) 99 78 20 +30937 66 18 18 E-mail: temper@chem.auth.gr www: http://users.auth.gr/temper ------=_NextPart_000_00A0_01C1BECA.6C6A94C0 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable

Thanks to all, for yours=20 comments.

My question  was:
 
I've been trying to = do a=20 geometry optimization using MP2/6-311++(d,p) (210 basis=20 functions)
 with GAUSSIAN = 98W A.11 but=20 I can't.
WHY?(I have an = ATHLON 1.6+GHz=20 with 512 MB memory and 30+ GB hard disk).
The operating system = is WINDOWS=20 2000.
I defined memory and = hard=20 disk:
 
%m=3D180MB
-------------------------------------------------
#p = mp2/6-311++(d,p) opt=20 scf=3Ddirect maxdisk=3D7000MB
-------------------------------------------------

The error from the output is shown = below:
(Enter=20 C:\G98W\l906.exe)
Frozen-core = derivative=20 calculation, NFC=3D 10 NFV=3D 0.
FulOut=3DF = Deriv=3DT=20 AODrv=3DT
MMem=3D 3 = MDisk=3D 18 MDiskD=3D=20 18
W3Min=3D 1270080 = MinDsk=3D=20 1759100 NBas6D=3D 216
NBas2D=3D 23697 = NTT=3D 23436=20 LenExt=3D 21464976
MDV=3D 23464976 = MDiskM=3D 1380=20 NBas2p=3D 23300
Disk-based = method using=20 ON**2 memory for 18 occupieds at a time.
Estimated = scratch disk=20 usage=3D 333638376 words.
IMap=3D 1 2 3 4 = 5 6 7 8 9 10=20 11 12 13 14 15 16 17 18 19 20
IMap=3D 21 22 23 = 24 25 26 27=20 28
Actual scratch = disk usage=3D=20 333205784 words.
JobTyp=3D1 Pass = 1: I=3D 11 to=20 28.
writwa
 
Can anyone give me = an advice?=20 Thanks in advance.
 

All the answers are = follow, and=20 thanks again:

*****
 
As far as I=20 know, Windows whatsoever is a 32bit operating system (still
some 16 = bit stuff=20 around?). Therefore, the size of a single file is limited
to ca. 2 = GByte.=20 Beyond that, you have to split your files. This procedure
is = described in the=20 handbook. Or have a look at the gaussian website at
www.gaussian.com, "Tech info".

Regards
Wolfgang=20 Roth
 
*****
 
G98W can only = handle scratch=20 files up to 2 GB, although it can use more than one. From your output, = it seems=20 that the MP2 calculation needs about 2.5 GB. What you have to do is to = split the=20 .rwf file into several (here two) portion (<2GB). See %rwf directive = in the=20 G98 help, for example: %rwf=3Dc:\1.rwf,1.9GB,c:\2.rwf,1.9GB, .... You = get the=20 idea?

Hope this=20 helps,

        Rainer=20 Koch.

PS: If in doubt, search the CCL archive for more = information, this=20 topic is discussed about every two months or = so...
 
*****
 
the file system of W 20000 does not = allow to=20 write large single file u should
separate the .rwf file
Just insert the=20 line %rwf=3Dc:\1\1,2000mb,c:\2\2,2000mb,c:\3\3,2000mb,c:\4\4,2000mb,= c:\5\5,2000mb
in the beginning of the = input.
u should first create the required = paths c:\1,=20 c:\2 etc
 
Panaghiotis Karamanis
 
*****
 
G98W is a 32 bit application and as = such is=20 limited to 2GB
pre file.  To exceed this you can specify the = RWF as a=20 compound
file

%rwf=3Da,245mw,b,245mw,c,245mw

up to a = maximum of=20 8 files.  Then the value for MaxDisk should
be set to the sum of = these=20 files, MaxDisk=3D735MW in my example.

   This will give = you the=20 best chance of completing this.

Cust.  Service = Doug
 
*****
 
I=20 suspect that the job is failing because the scratch file (*.rwf) is = exceeding=20 2GB.  Remember, Gaussian98 can use up to 16GB of h-drive space but = Win2000=20 can only use 2GB files.  Try this:
 
%rwf=3Da,240MW,b,240MW,c,240MW,d,240MW,
%nosave
%m=3D180MB
#p=20 mp2/6-311++(d,p) opt scf=3Ddirect maxdisk=3D7000MB
 
Good=20 luck,
 
Phil=20 Matz
 
*****
 
 
You = ran out of=20 space in your rw file.  Windows rw files can only be 2GB.  You = need=20 about 3GB.
 
Using the options = specified in the=20 G98W manual, you can create multiple rw files.  Use that to make 2, = 2GB rw=20 files and the job should get past your present error OK.
 
Jim Kress
 
*****
 
Dear = Vasilios,
Your problem = looks identical=20 to one which has been asked
and answered = many times on=20 the CCL.  You need to break
up your rwf file = into=20 Gaussian-sized chunks.  Rather than
tell you the = answer, I'll=20 tell you how to find the  answer,
which could have = saved you a=20 posting in the first place.
Think of this when = future problems=20 arise:  Go to the CCL
web page and search = the archives=20 for keyword "writwa",
which is the tell-tale = part of=20 your error message.  You
will see there is a = simple=20 solution.
David Anick MD = PhD
David.Anick@gte.net
 
*****
 
it needs more disk = space. Increase=20 your maxdisk (check the DEfault.ROute, too). I dont know about g98W, but = in=20 linux you have to assign diferent file names to use as schratch (eg.=20 %rwf=3Da,200mw,b,200mw,c,200mw,d,200mw )

take=20 care,

Guilherme
Dinamica = Sonora
 
*****
 
Hi = Vasilios.


some=20 operating systems have a filesize limit of 2GB.  Try the = following:
a)=20 MaxDisk=3D2040MB
or
b) splitting the RWF file into several pieces=20 <2GB

e.g.

%RWF=3D/scr/a,2040MB,/scr/b,2040MB,/scr/c,2040= MB=20 ...

good luck.

 Juan
 
Juan Pablo = Senosiain
 
*****
 
Your = disk usage is=20 about 1/3 gigawords, or about 2.33 GB.  Although this is
well = within the=20 size of your hard disk, it's above the per-file limit of 2GB
that = some=20 operating systems have, including Microsoft Windows.
 
There = is a=20 work-around.  Put the following line under your=20 memory
specification:
%rwf=3Dr1,240mw,r2,240mw,r3,240mw,r4,-1
Th= is will=20 create files of 240 megawords (1960 MB), each of which is below
the = 2GB=20 limit, with the names r1.rwf, r2.rwf, r3.rwf, and r4.rwf.  = When
r1.rwf=20 fills up Gaussian will move to r2.rwf and so on.  =
 
Hope this=20 helps.
--David Shobe
Sud-Chemie Inc.
phone (502)=20 634-7409
fax     (502) 634-7724
email  = dshobe@sud-chemieinc.com

Don't bother flaming me: I'm = behind a=20 firewall.
 
*****
 
Dear Vasilios!
Try to use the PC GAMESS!
 
Best regards,
Alex Granovsky
 
*****
 
Dear Vasilios:

It seems to be a problem with the scratch = disk space.=20 Namely, some versions
of Gaussian (G98W included) are not able to = handle the=20 files larger than 2GB
(due to the wrong compiling options). To = overcome this=20 you should supply
some additional input cards, specifying the = locations and=20 sizes of these
scratch files. See, please, the beginning of the = sample input=20 file:

%rwf=3DF:\a,2GB,F:\b,2GB,F:\c,2GB,F:\d,2GB,F:\e,2GB,F:\f,2GB= ,F:\g,2GB,F:\h,2GB
%nosave
%chk=3Dfn13mp3_trans.chk
%mem=3D1400M= B

#N=20 QCISD /6-31+G(d) SCF=3D(MAXCYCLE=3D900) geom=3Dcheck guess=3Dread
# = POP=3DREG GFINPUT=20 IOP(6/7=3D3) pop=3Dminimal scf=3Ddirect

fn13

0,1

In = the above=20 example a,b,c,d,e,f,g,h are the file names, 2GB each. The
length of = this=20 record is limited, as I remember to 76 (or 80) characters.
Until to = revision=20 A.7 there is no possibility to specify any additional %rwf
cards, = thus to me=20 the scratch disk space is limited to 8X2GB=3D16GB.

Another thing = is that=20 MP2 jobs are very sensitive to the main memory amount,
thus if you = have 500MB=20 of main memory, it's better to set this memory card
about 400MB. = Never put it=20 450MB or more, due to the extensive swapping
resulting in a very low=20 perfomance.

I hope this will help.

Andrus = Metsala
 
*****
 
Dear = Vasilios I.=20 Teberekidis

The file size for G98 on a 32 bit OS is limited to 8=20 pieces
of about 2Gb size to give totally about 16 Gb.

  = insert=20 the following line as link0 line in your=20 input
file:

%rwf=3D/path/1,1900mb,/path/2,1900mb,/path/3,1900mb= ,/path/4,1900mb,/path/4,1900mb,/path/5,1900mb,/path/6,1900mb,/path/7,1900= mb,path/8,-1

/path/=20 is the path to a scratch directory - such as /scr/

the rwf file = will be=20 split into 1900 mb pieces with the
names 1.rwf, 2.rwf = .....

good=20 luck
Hans-Ullrich Siehl
 
*****
 
Hi,
The writwa at the end of the output = mentions that=20 you have run out
of scratch disk space. You may try one of two = things: (1)=20 split the
scratch file into 3-5 partitions, or (2) optimise the = geometry at=20 a
lower or DFT level, and perform a single point MP2=20 calculation.

Cheers,
Balakrishnan
Balakrishnan=20 Viswanathan
Department of Chemistry
Dalhousie = University
Halifax, Nova=20 Scotia
Canada B3H 4J3
(902) 494-7021
bviswan@chem1.chem.dal.ca
 
 
That's = all.
 
 = Postgraduate (Ph.D) Student
Vasilios = I.=20 Teberekidis
Laboratory of Applied Quantum Chemistry
Aristotle = University=20 of Thessaloniki (Greece)
Tel.:(+30 31) 99 78=20 20
        +30937 66 18 = 18
E-mail: temper@chem.auth.gr
www: http://users.auth.gr/temper
------=_NextPart_000_00A0_01C1BECA.6C6A94C0-- From chemistry-request@server.ccl.net Tue Feb 26 10:29:46 2002 Received: from mail.zrz.tu-berlin.de ([130.149.4.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1QFTj523563 for ; Tue, 26 Feb 2002 10:29:46 -0500 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail.zrz.tu-berlin.de with esmtp (exim-3.35) id 16fjXW-00024o-00; Tue, 26 Feb 2002 16:29:14 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.35) id 16fjXV-0004kc-00; Tue, 26 Feb 2002 16:29:13 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <3C7BA287.C6DA976D@kvl.dk> References: <3C7BA287.C6DA976D@kvl.dk> Date: Tue, 26 Feb 2002 16:29:12 +0100 To: Peter Waaben Thulstrup From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:G98: How to extract force constants from output? Cc: chemistry@ccl.net Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g1QFTk523564 >Dear CCL > >Can anybody give simple instructions on extracting stretching and >bending force constants for individual bonds from G98 output. > ... you can only "see" them in the checkpoint file, so use formchk to make it human-readable, and then you see the force constant matrix in cartesian coordinates. To get stretch, bend etc. force coordinates, you have to define (in cartesian coordinates) a displacement vector for this stretch, bend etc. Then the force constant comes out of matrix-vector-algebra (using the cartesian force const. matrix and the displacement vector). +---------------------------------+----------------------------------+ | Prof. Christoph van Wüllen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universität Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Straße des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+----------------------------------+ -- From chemistry-request@server.ccl.net Tue Feb 26 12:05:40 2002 Received: from jeeves.ccdc.cam.ac.uk ([131.111.113.44]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1QH5d525338 for ; Tue, 26 Feb 2002 12:05:39 -0500 Received: from sun14.ccdc.cam.ac.uk ([131.111.113.48] helo=ccdc.cam.ac.uk) by jeeves.ccdc.cam.ac.uk with esmtp (Exim 3.12 #1 (Debian)) id 16fl2N-0004Ab-00; Tue, 26 Feb 2002 17:05:11 +0000 Sender: jaccos@ccl.net Message-ID: <3C7BC047.58FD9F9C@ccdc.cam.ac.uk> Date: Tue, 26 Feb 2002 17:05:11 +0000 From: Jacco van de Streek Organization: CCDC X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.8 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: Richard Gillilan CC: "'chemistry@ccl.net'" Subject: Re: CCL:Hydrophobic ligands (was molecular docking startup) References: <3C7B9A48.C2E4A7F2@cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Richard Gillilan wrote: > > Interesting. Anyone else have comments on docking hydrophobic ligands? > > Right away I can think of a couple reasons why hydrophobics would be > difficult. Without strong, directed polar interactions, the binding > site would naturally be shallower and less well defined. Docking > programs without a good solvent model may also contribute to the > problem, but I wonder if that is really a significant factor or not. > > There was a paper just out in J. Comp. Chem. about the failure of > point charge models to correctly reproduce crystal lattices of n-alkanes: > > "On the irrelevance of electrostatics for the crystal structures and > polymorphism of long even n-alkanes" > Jacco Van de Streek, Paul Verwer, Piet Bennema, Elias Vlieg > (JCP v23 #3 2002) > > Anyone worked with the Thermal Motion Forcefield (TMFF) mentioned > in the article, or know where the paper is supposed to come out? The paper has been accepted for publication in Acta Crystallographica section B, the revised manuscript has just been sent to the referees again. I would like to stress that TMFF was developed only as a means to show that thermal motion explains the structural discrepancies between experimental and statically minimised crystal structures for long even n-alkanes (till now, it had either been published that thermal motion was irrelevant, or that electrostatics might be paramount: both views will lead to wrong structures and wrong relative energies) and that is the only thing we claim it can do (very important if you do polymorph predictions and want to minimise approx. 10,000 crystal structures per conformation per compound and compare each to an unindexed experimental powder pattern, triclinic, one long unit cell axis, two short). Relative energies between two polymorphs are also greatly improved, but we don't know about absolute energies. It would be nice if someone could validate the usefulness of TMFF outside this rather narrow area of application. Implementing TMFF in GOLD is technically feasible (I just checked with one of the programmers: by pure chance, GOLD happens to be partially developed here at the Cambridge Crystallographic Data Centre where I work now, the work on TMFF was done at the University of Nijmegen). Note though, that TMFF has only been parameterised for Carbon and Hydrogen. Jacco. -- Jacco van de Streek Research Scientist Cambridge Crystallographic Data Centre Cambridge United Kingdom From chemistry-request@server.ccl.net Tue Feb 26 14:21:48 2002 Received: from red.csi.cam.ac.uk (exim@[131.111.8.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1QJLm527380 for ; Tue, 26 Feb 2002 14:21:48 -0500 Received: from bjc32 (helo=localhost) by red.csi.cam.ac.uk with local-esmtp (Exim 3.34 #1) id 16fnAA-00039g-00 for chemistry@ccl.net; Tue, 26 Feb 2002 19:21:22 +0000 Date: Tue, 26 Feb 2002 19:21:22 +0000 (GMT) From: Ben Carrington X-X-Sender: To: Subject: Normal Modes for large proteins Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Can anyone suggest how I go about performing normal modes calculations on large systems - protein complexes to be exact. At the moment I cannot get any programs to run due to the large amount of memory needed. Can I split this calculation up? Yours hopefully, Ben bjc32@cam.ac.uk From chemistry-request@server.ccl.net Tue Feb 26 15:27:01 2002 Received: from mail.rpi.edu ([128.113.22.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1QKR1528299 for ; Tue, 26 Feb 2002 15:27:01 -0500 Received: from rpi.edu (exothermic-04.dynamic.rpi.edu [128.113.21.159]) by mail.rpi.edu (8.12.1/8.12.1) with ESMTP id g1QKQYdp065416 for ; Tue, 26 Feb 2002 15:26:35 -0500 Message-ID: <3C7BEF91.721FF997@rpi.edu> Date: Tue, 26 Feb 2002 15:26:57 -0500 From: "Curt M. Breneman" X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCG Graduate Student Excellence Award Winners - Orlando, 2002 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Scanned-By: MIMEDefang 2.3 (www dot roaringpenguin dot com slash mimedefang) The American Chemical Society's (ACS) Division of Computers and Chemistry (COMP) and Chemical Computing Group (CCG), are pleased to announce the winners of the CCG Excellence Awards for the Spring ACS National Meeting, to be held in Orlando, FL from April 7-11, 2002. In alphabetical order, the winners are: Thomas Dick for the paper entitled “Computational Modeling of Brine to aid CO2 Sequestration Research”. Co-authors on the paper are Pranav Dalal and Jeffry Madura. Mr. Dick is a graduate student in Prof. Madura’s labs in the Department of Chemistry and Biochemistry at Duquesne University in Pittsburgh, PA. Benoit Leblanc for the paper entitled “Mixing Monte Carlo moves more efficiently with an evolutionary algorithm”. Co-authors on the paper are Herve Toulhoat, Bertrand Braunsweig, and Evelyne Lutton. Mr. Leblanc is a graduate student in Computer Science at IFP (Institut Francais du Petrole) in Rueil-Malmaison, France, and is advised by his co-authors. Viera Lukacova for the paper entitled “Implementation of Multiple Binding Modes in CoMFA”. Ms. Lukacova’s co-author on the paper is Stefan Balaz. Ms. Lukacova is a graduate student in Prof. Stefan Balaz’ labs in the Department of Pharmaceutical Sciences, College of Pharmacy, at North Dakota State University. Sabine Schefzick for the paper entitled “Theoretical Ligand Distortions in Chiral Catalysts: Can molecular deformations enhance a catalyst’s chirality content?”. Co-author on the paper is Prof. Kenny Lipkowitz. Ms. Schefzick is a graduate student in Prof. Lipkowitz’ labs in the Department of Chemistry at Indiana University Purdue University-Indianapolis (IUPUI) in Indianapolis, Indiana. Xuelin Wang for the paper entitled “Error Analysis in Density Functional Theory: Atomization Energies.” Co-authoring the paper is Prof. Angela K. Wilson. Mr. Wang is a graduate student in Prof. Wilson’s labs in the Department of Chemistry at the University of North Texas, in Denton, TX. The CCG Excellence Awards have been created to stimulate graduate student participation in COMP Division activities (symposia and poster sessions) at ACS National Meetings. Winners will receive a one-year software license of CCG's MOE (Molecular Operating Environment) for their academic research groups, in addition to travel costs associated with attending an ACS National Meeting to present their research. Awardees are chosen on the basis of the quality and significance of the research to be presented and the strength of the supporting materials. Please join us in congratulating the winners of the CCG Excellence Awards for the Chicago ACS Meeting. We will present the awards at the COMP Poster Session (Tuesday Evening in McCormick Place South). Applications for the next round of CCG Excellence Awards will be accepted shortly. Application for these awards is a two-step process. First, one must submit an abstract through the ACS OASYS system for online paper submissions. Secondly, an application for the Award must be submitted to the Treasurer of the COMP division for consideration. Deadlines for these two steps are different to allow graduate students time to compile the additional paperwork needed to complete the application. Deadlines for the 2002 Fall National Meeting to be held in Boston, MA, will be announced shortly. Online submission of abstracts to the Boston Meeting will be opened sometime in mid-March and close at midnight eastern time on Monday April 1, 2002. The website will be www.acs.org/meetings/boston2002. Supporting materials must include an extended 1-2 page abstract for your paper along with a letter of support > from your research advisor, a two-page CV and a personal statement. Deadline for supporting information will be announced after the Orlando National Meeting is completed. All graduate students are encouraged to submit applications for the Awards. Students from the same research group are encouraged to apply. Students from research groups that have won awards at previous ACS meetings are also encouraged to submit applications. Awards will be given only to those individuals making presentations, and not co-authors. Send all application materials to: Prof. Curt M. Breneman; Treasurer, ACS COMP Division; RPI Department of Chemistry; 110 8th St.; Troy, NY 12180 From chemistry-request@server.ccl.net Tue Feb 26 16:13:36 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1QLDa528997 for ; Tue, 26 Feb 2002 16:13:36 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 16foqr-0003zZ-00; Tue, 26 Feb 2002 21:09:33 +0000 Date: Tue, 26 Feb 2002 21:09:33 +0000 (GMT) From: Szilveszter Juhos To: Ben Carrington cc: chemistry@ccl.net Subject: Re: CCL:Normal Modes for large proteins In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 26 Feb 2002, Ben Carrington wrote: > get any programs to run due to the large amount of memory needed. Can I > split this calculation up? As a novice in MD I can say that likely not :( But why are you running out of memory? Is it beacuse you do not have enough physical memory (that should not be a problem novadays) or because your user resource is limited (check the 'limit' command using tcsh or 'ulimit -a' with bash)? If you give more details about the error you get... Szilva From chemistry-request@server.ccl.net Tue Feb 26 18:03:40 2002 Received: from smtp2.octa4.net.au ([203.112.96.25]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g1QN3d531970 for ; Tue, 26 Feb 2002 18:03:39 -0500 Received: (qmail 1011 invoked from network); 26 Feb 2002 23:03:15 -0000 Received: from dwn-dialport7.octa4.net.au (HELO octa4.net.au) (203.112.97.7) by smtp2.octa4.net.au with SMTP; 26 Feb 2002 23:03:15 -0000 Received: by octa4.net.au (sSMTP sendmail emulation); Wed, 27 Feb 2002 08:31:08 +0930 Date: Wed, 27 Feb 2002 08:31:08 +0930 From: Brian Salter-Duke To: chemistry@ccl.net Subject: Mopac93 and Linux/g77 Message-ID: <20020227083108.A1476@BSALTERDUKE1> Mail-Followup-To: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i I have had mopac93 run from web pages via cgi as a treaching aid. Recently that machine died and I have had to move the web pages to linux. I can not compile mopac93 successfully. I compiled mopac7 OK using f2c/gcc as described on the WebMO pages. g77 causes conflicts with the SECOND(N) routine which it thinks is intrinsic. I guess one could get around this, but f2c/gcc works. mopac93 is similar. f2c/gcc gives an executable, but the output soon turns to garbage. Has anyone managed to get a correct running executable of mopac93 on linux? When running this code and others from web pages I need a simple queuing system. I used to use NQS but this is overkill and it seems to have little support these days. I failed to compile it under tru64 for example after running it for years on the same machine running DEC OSF1. Does anyone know of a simple queuing system for linux? I want a single queue running just one job at a time. Being able to inspect the queue and delete items would be nice, but nothing fancier is required. Regards to all, Brian. -- Brian Salter-Duke (Brian Duke) b_duke@octa4.net.au Honorary Fellow in Chemistry, NT University, Darwin, NT 0909, Australia. Phone 08-89881600. Fax 08-89881302. http://lacebark.ntu.edu.au/ From chemistry-request@server.ccl.net Tue Feb 26 20:47:59 2002 Received: from smtp7.jaring.my ([61.6.32.57]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1R1lw506440 for ; Tue, 26 Feb 2002 20:47:58 -0500 Received: from vplaces.net (j67.kch20.jaring.my [161.142.55.81]) by smtp7.jaring.my (8.11.4/8.11.4) with ESMTP id g1R1l7p24824 for ; Wed, 27 Feb 2002 09:47:14 +0800 (MYT) Message-ID: <3C7C3C49.8B7D8CF3@vplaces.net> Date: Wed, 27 Feb 2002 09:54:17 +0800 From: Rowyna X-Mailer: Mozilla 4.75 [en] (Win98; U) X-Accept-Language: en,pdf MIME-Version: 1.0 To: CCL Subject: calculating dihedral angle Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I would be grateful if somebody could suggest any programs/utilities/scripts which can be used to calculate all the possible dihedral angles of a given molecule or structure. I'm interested in using such utilities, hopefully without charge. Maybe I could write a script for the calculations but I'm not sure how to start with that so perhaps an existing program would suit me better. It would be a lot of help and much thanks in advance. Rowyna K. Institute of Biological Sciences, UM Malaysia