From chemistry-request@server.ccl.net Thu Nov  7 03:18:57 2002
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From: Jamie Platts <Platts@Cardiff.ac.uk>
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To: Connie Chang <cc236@cornell.edu>
cc: chemistry@ccl.net
Subject: Re: CCL:visualizing HOMO/LUMO with Gaussian98W
In-Reply-To: <3DC97708.88C5A4A0@cornell.edu>
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  Hi Connie - you might like to try out Molekel, available from

http://www.cscs.ch/molekel/  

or Molden

http://www.cmbi.kun.nl/~schaft/molden/molden.html

both of which produce very nice graphical outputs of orbitals, potentials,
and other properties. Molden is also a nice way of keep track of
optimisations, frequencies etc.

  Regards,

  Jamie

----------------------------------------------------------
  Jamie Platts 							 
  Dept. of Chemistry  		Phone: +44 (0) 2920 874950		 
  Cardiff University 	 	Email: platts@cf.ac.uk		 
  P.O. Box 912 			FAX:   +44 (0) 2920 874030		 
  Cardiff CF10 3TB 		www.cf.ac.uk/chemy

> Hi all --
> 
> Is there a way to plot the shape of the HOMO and LUMO level using
> Gaussian98W?
> 
> thanks,
> connie
> 
> 
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> 
> 
> 
> 
> 


From chemistry-request@server.ccl.net Thu Nov  7 10:44:44 2002
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From: Marcin Krol <mykrol@cyf-kr.edu.pl>
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Subject: CHARMM question
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Dear CHARMM users,
When generating a really large water cube I got LEVEL -4 WARNING FROM
<ALLDT> DATA STRUCTURE REALLOCATED IN ALLDT
What parameter in fcm should I increase to get rid of the error?
Thank you in advance
Marcin


From chemistry-request@server.ccl.net Wed Nov  6 21:39:41 2002
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Subject: AutodockTools Question
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Dear CCLers,
   		I'm using AutoDockTools.As my receptor misses about 20 residues in the middle region(but far away from my pocket),it looks like owning two peptide chains.When I grid in ADT,there is such error message:"non-integer charge:Gly142,Val177,Lys198,Ile431".I have checked and found that these are exactly the four terminal residues.Then I fixed the residues by add H to terminal N and O.Unfortunately,the problem remains.How should I deal with such case?
Best Regards!
---------------------
Liu Zhi-Guo
Ph.D candidate
Drug Design & Discovery Center
Shanghai Institute of Materia Medica
Shanghai,in China





From chemistry-request@server.ccl.net Thu Nov  7 10:55:35 2002
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Subject: CCL: Computational Library Design
Date: Thu, 7 Nov 2002 16:05:23 -0000
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Hi all,=20


Sorry to bother you yet again, but I was wondering if any one knows of a =
program ( and cost) that can be used to generate lots of molecules based =
on a common substructure?=20

At the moment I am carrying out docking and qsar calculations and would =
like to generate a library of compounds that I could screen based on my =
results.=20

Thanks for all your help

Iain=20

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<DIV><FONT face=3DArial size=3D2>Hi all, </FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Sorry to bother you yet again, but I =
was wondering=20
if any one knows of a program ( and cost) that can be used to generate =
lots of=20
molecules based on a common substructure? </FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>At the moment I am carrying out docking =
and qsar=20
calculations and would like to generate a library of compounds that I =
could=20
screen based on my results. </FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thanks for all your help</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Iain </FONT></DIV></BODY></HTML>

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From chemistry-request@server.ccl.net Thu Nov  7 10:52:08 2002
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From: wei <weiz@mail.rochester.edu>
Reply-To: weiz@mail.rochester.edu
Organization: university of rochester
To: chemistry@ccl.net
Subject: charmm compilation problem
Date: Thu, 7 Nov 2002 10:51:24 -0500
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Hi,
   I want to compile charmm on redhat linux with gnu. and I type the command 
"install.com gnu large", it didn't create the executable. and gave out 
followling information in gnu.log. can anybody tell me  if I have to modify 
some thing and how to do it?

**************************************************************************
**CHARMM Build on gnu Thu Nov 7 10:46:15 EST 2002
/home/shiva/charmm/c27b1/tool/preflx 
/home/shiva/charmm/c27b1/source/adumb/cmds.src
Segmentation fault (core dumped)
g77 -malign-double -fno-f2c -fno-backslash -O2 -fugly-complex -fno-globals 
-Wno-globals -DGNU  -c cmds.f
cmds.f: In subroutine `numfil':
cmds.f:1480: 
         IMPLICIT NONE
         ^
End of source file before end of block started at (^)
cmds.f:1472: 
         SUBROUTINE NUMFIL(IPT,JPT,INM,JNM,LIS,
                           1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `ipt' at (2) [initially seen at 
(1)]
cmds.f:1472: 
         SUBROUTINE NUMFIL(IPT,JPT,INM,JNM,LIS,
                               1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `jpt' at (2) [initially seen at 
(1)]
cmds.f:1472: 
         SUBROUTINE NUMFIL(IPT,JPT,INM,JNM,LIS,
                                   1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `inm' at (2) [initially seen at 
(1)]
cmds.f:1472: 
         SUBROUTINE NUMFIL(IPT,JPT,INM,JNM,LIS,
                                       1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `jnm' at (2) [initially seen at 
(1)]
cmds.f:1472: 
         SUBROUTINE NUMFIL(IPT,JPT,INM,JNM,LIS,
                                           1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `lis' at (2) [initially seen at 
(1)]
cmds.f:1473: 
        &                  RMN,KMN,RMX,KMX,FMX,TCN,AVE,EXP)
                           1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `rmn' at (2) [initially seen at 
(1)]
cmds.f:1473: 
        &                  RMN,KMN,RMX,KMX,FMX,TCN,AVE,EXP)
                               1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `kmn' at (2) [initially seen at 
(1)]
cmds.f:1473: 
        &                  RMN,KMN,RMX,KMX,FMX,TCN,AVE,EXP)
                                   1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `rmx' at (2) [initially seen at 
(1)]
cmds.f:1473: 
        &                  RMN,KMN,RMX,KMX,FMX,TCN,AVE,EXP)
                                       1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `kmx' at (2) [initially seen at 
(1)]
cmds.f:1473: 
        &                  RMN,KMN,RMX,KMX,FMX,TCN,AVE,EXP)
                                           1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `fmx' at (2) [initially seen at 
(1)]
cmds.f:1473: 
        &                  RMN,KMN,RMX,KMX,FMX,TCN,AVE,EXP)
                                               1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `tcn' at (2) [initially seen at 
(1)]
cmds.f:1473: 
        &                  RMN,KMN,RMX,KMX,FMX,TCN,AVE,EXP)
                                                   1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `ave' at (2) [initially seen at 
(1)]
cmds.f:1473: 
        &                  RMN,KMN,RMX,KMX,FMX,TCN,AVE,EXP)
                                                       1
cmds.f:1758: (continued):
         COMMON /PNOE/ c0x ,c0y ,c0z, QPNOE
   2
Invalid declaration of or reference to symbol `exp' at (2) [initially seen at 
(1)]
make: *** [/home/shiva/charmm/c27b1/lib/gnu/adumb.a(cmds.o)] Error 1
****************************************************************


From chemistry-request@server.ccl.net Thu Nov  7 13:54:49 2002
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From: "Liu, Zhanwu" <LiuxZx@anes.upmc.edu>
To: "'chemistry@ccl.net'" <chemistry@ccl.net>
Subject: Br in 6-31G using Gaussian98
Date: Thu, 7 Nov 2002 13:54:47 -0500 
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Dear all,

In the reference of Gaussian 98, it is indicated that 6-31G basis sets are
not applicable to Br atom. But when I using this basis sets (6-31G)  for
calculation of a molecule containing Br, it worked. Buy using the "Gfprint"
keyword in Gaussian input file, I got the basis function used for Br, it
contains 6 s functions (8,2,1,1,1,1 gaussians respectively), 4 p functions
(6,3,1,1 gaussians, respectively) and 1 6D functions (5 gaussians).  Any one
where these functions come from?  If using this, can I get accurate results
for my Br-containing molecules?

Thanks a lot!

Yours Zhanwu

-----------------------------
Zhanwu Liu, Ph.D.
Department of Anesthesiology
University of Pittsburgh
Phone: 412-648-9137
Fax:   412-648-9587


From chemistry-request@server.ccl.net Thu Nov  7 16:05:23 2002
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From: "Pandey, Jaya" <JPandey@chla.usc.edu>
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Subject: Autodock
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Dear All,

I am trying to use autodock to generate some inhibitors for my receptor. I
work in UNIX and do not visualise the proceedings of the docking. Is there a
program that has a window to visualise like VEGA the proceedings of the
auotdocking steps?? Please reply and help as I am not really able to
understand and move on much.

Thanks

jaya

From chemistry-request@server.ccl.net Thu Nov  7 13:55:44 2002
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Date: Thu, 7 Nov 2002 14:53:47 -0400
Sender: Robert Flight <l72k6@unb.ca>
From: Robert Flight <l72k6@unb.ca>
To: "zgleo" <zgliu@sohu.com>, Computational Chemistry List <chemistry@ccl.net>
Cc: Ghislain Deslongchamps <ghislain@unb.ca>, Larry Calhoun <calhoun@unb.ca>
X-EXP32-SerialNo: 00003025, 00003442
Subject: RE: CCL:AutodockTools Question
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Hi Liu,

I have the same problem in my system where I have a break in the amino acid 
sequence, and I get an residue with a non-integral charge.  If the charge is 
not off by much (say less than 0.5 charge units) I just adjust the charge on 
the individual atoms of the residue so that the total charge adds up to the 
proper integer (0,1,2, whatever), this shouldnt affect the docking results too 
much if the residues are outside of the Grid box used for docking.  If you are 
using Mol2 files to prepare your receptor it is really easy to modify using a 
text editor (the PDBQS format doesnt label the individual residues).

You might also want to check the original file and make sure that the bonding 
between atoms is right, as this will also affect the charge calculation.

Hope this helps.

Cheers,

Robert

>===== Original Message From "zgleo" <zgliu@sohu.com> =====
>Dear CCLers,
>   		I'm using AutoDockTools.As my receptor misses about 20 residues in the 
middle region(but far away from my pocket),it looks like owning two peptide 
chains.When I grid in ADT,there is such error message:"non-integer 
charge:Gly142,Val177,Lys198,Ile431".I have checked and found that these are 
exactly the four terminal residues.Then I fixed the residues by add H to 
terminal N and O.Unfortunately,the problem remains.How should I deal with such 
case?
>Best Regards!
>---------------------
>Liu Zhi-Guo
>Ph.D candidate
>Drug Design & Discovery Center
>Shanghai Institute of Materia Medica
>Shanghai,in China

********************************
Robert Flight
Masters Student
Department of Chemistry
University of New Brunswick
Fredericton, NB  Canada  E3B 6E2
e-mail: L72K6@unb.ca
 
********************************

"What is wanted is not the will to believe but the wish to find out, which is the exact opposite." -- Bertrand Russell



From chemistry-request@server.ccl.net Thu Nov  7 14:04:09 2002
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Dear all:
    I tried to use NMR module  of CHARMM to calculate order parameters, 
but after I read the psf and trajectories file and enter NMR sub modle. 
Charmm report the following error message:
      ***** LEVEL -4 WARNING FROM <ALLHP> *****
      ***** Bad length was passed to FREEHP
      ******************************************
  what's the matter? Shall I do any additional prepared work?

Chen Hao




From chemistry-request@server.ccl.net Thu Nov  7 14:46:29 2002
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Subject: Free Protein Builder
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 02:46:08 PM
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I am looking for freeware (or shareware) which can reasonably build protein
motifs.  That is, I want to build a peptide sequence which has certain
residues in an alpha-helical arrangement followed by say extended
conformation, etc.  I have a secondary structure prediction of a peptide
sequence and want to examine families of tertiary structures based on that
secondary structure prediction.

Two dogpile searches failed to turn up anything.  So I would be very
grateful for any pointers to some useful software.

Thanks!
*****************************************************************
Dr. Mark A. Zottola
PET Director of Computational Chemistry and Materials
Army Research Laboratory MSRC
PB 191 939-I Beards Hill Road
Aberdeen  MD 21001
VOICE: 410 278 7250     FAX: 410 297 9521