SOMFA and CSSR file format

From chemistry-request@server.ccl.net Sun Aug 19 13:40:50 2001 Received: from hotmail.com ([64.4.8.47]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7JHenM07010 for ; Sun, 19 Aug 2001 13:40:49 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sun, 19 Aug 2001 10:40:44 -0700 X-Originating-IP: [164.111.194.199] Reply-To: "Jason Lott" From: "Jason Lott" To: Subject: Matlab port of STEPIT Date: Sun, 19 Aug 2001 12:44:29 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0013_01C128AC.B032F4E0" 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 Message-ID: X-OriginalArrivalTime: 19 Aug 2001 17:40:44.0248 (UTC) FILETIME=[128DCD80:01C128D6] This is a multi-part message in MIME format. ------=_NextPart_000_0013_01C128AC.B032F4E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all, I've recently completed a beta port of STEPIT to Matlab. STEPIT is a = fitting program originally written by J. Chandler in Fortran many years = ago. For those of you interested in working with STEPIT in a Matlab = environment, this is now possible. The program can be downloaded at: http://www.ccl.net/cca/software/SOURCES/FORTRAN/simplex/MATLAB_STEPIT/ or ftp://ftp.ccl.net/pub/chemistry/software/SOURCES/FORTRAN/simplex/MATLAB_S= TEPIT/ Please note that all of the files must be downloaded into the same = folder in order to use this program. Please consult the readme for more = information about program use, modifications, etc. And please, this is a = work in progress--please report any bugs, fixes, problems, etc to me, = and I will get on it.=20 Cheers, Jason Lott University of Alabama at Birmingham August 19 2001 hoffa@uab.edu ------=_NextPart_000_0013_01C128AC.B032F4E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello all,

I've recently completed a beta port of STEPIT to = Matlab.=20 STEPIT is a fitting program originally written by J. Chandler in Fortran = many=20 years ago. For those of you interested in working with STEPIT in a = Matlab=20 environment, this is now possible. The program can be downloaded=20 at:

http://www.ccl.net/cca/software/SOURCES/FORTRAN/simplex/MATLAB_STE= PIT/

ftp://ftp.ccl.net/pub/chemistry/software/SOURCES/FORTRAN/= simplex/MATLAB_STEPIT/

Please note that all of the files must be downloaded = into the=20 same folder in order to use this program. Please consult the readme for = more=20 information about program use, modifications, etc. And please, this is a = work in=20 progress--please report any bugs, fixes, problems, etc to me, and I will = get on=20 it.

Cheers,

Jason Lott

University of Alabama at Birmingham

August 19 2001

hoffa@uab.edu

------=_NextPart_000_0013_01C128AC.B032F4E0-- From chemistry-request@server.ccl.net Mon Aug 20 00:42:40 2001 Received: from exstudent9.city.unisa.edu.au ([130.220.84.78]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7K4gYM25201 for ; Mon, 20 Aug 2001 00:42:35 -0400 Received: by exstudent9.city.unisa.edu.au with Internet Mail Service (5.5.2653.19) id ; Mon, 20 Aug 2001 14:12:29 +0930 Message-ID: From: "Sorich, Michael Joseph - SORMJ001" To: "'chemistry@ccl.net'" Subject: SOMFA and CSSR file format Date: Mon, 20 Aug 2001 14:12:26 +0930 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C12932.82A5EBA0" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C12932.82A5EBA0 Content-Type: text/plain Hello I have been attempting to use SOMFA, a 3D QSAR program. Superimposed molecules must be entered in CSSR (or XR) file format. I have molecules aligned in the mdl SD and sybyl MOL2 formats. I have used Babel, Cerius2 and Mol2Mol to convert to the CSSR format. When entered into the SOMFA program, however, all these converted files generate errors (eg "Error reading atom data"). 1) Has anyone else had this problem and if so, is there a solution? 2) Does anyone have any information on how the CSSR files are formatted, so I may interpret the error messages generated. Thanks for your time Michael Sorich PhD Student University of South Australia Email:SORMJ001@students.unisa.edu.au or mike_sorich@hotmail.com ------_=_NextPart_001_01C12932.82A5EBA0 Content-Type: text/html SOMFA and CSSR file format

Hello

I have been attempting to use SOMFA, a 3D QSAR program.
Superimposed molecules must be entered in CSSR (or XR) file format.
I have molecules aligned in the mdl SD and sybyl MOL2 formats.
I have used Babel, Cerius2 and Mol2Mol to convert to the CSSR
format. When entered into the SOMFA program, however, all these
converted files generate errors (eg "Error reading atom data").

1) Has anyone else had this problem and if so, is there a
solution?

2) Does anyone have any information on how the CSSR files
are formatted, so I may interpret the error messages generated.

Thanks for your time

Michael Sorich
PhD Student
University of South Australia

Email:SORMJ001@students.unisa.edu.au
or mike_sorich@hotmail.com

------_=_NextPart_001_01C12932.82A5EBA0-- From chemistry-request@server.ccl.net Mon Aug 20 09:50:09 2001 Received: from public.uni-hamburg.de ([134.100.32.55]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7KDo8M16809 for ; Mon, 20 Aug 2001 09:50:08 -0400 Received: from hfuss (hfuss.chemie.uni-hamburg.de [134.100.204.17]) by public.uni-hamburg.de (8.8.8/8.8.8) with SMTP id PAA64850; Mon, 20 Aug 2001 15:50:07 +0200 Message-ID: <200108201552080880.009480F8@public.uni-hamburg.de> X-Mailer: Calypso Version 2.40.40 Date: Mon, 20 Aug 2001 15:52:08 +0200 From: "Frank Hoffmann" To: chemistry@ccl.net Subject: CCL: different MNDO parameter sets and partial charges Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f7KDo9M16810 Dear CCLers, I'm new in the field of modelling and I want to know something more about the MNDO semiempirical method. Performing calculations of geometry optimization, partial charges and vibrational frequencies of a particular molecule with the the same method (MNDO) but with different programs results in different values for bond lenghts/angles, charges, and modes. Obviously, the different software packages use different MNDO parameter sets. I want to know, if they have names, what sets are usually used (is there a standard or reference set?), and what the "best" among them is; best means, of course, not a general variable, but in my special case I would like to calculate accurate partial charges. Apropos: which other semiempirical or ab initio method do you prefer for the calculation of partial charges normally and why? So, this include implicit the question how accurate a non-observable value can be... Hope, these are not to many questions for one mail... Thank you very much in advance! Frank From chemistry-request@server.ccl.net Mon Aug 20 12:10:39 2001 Received: from phm.utoronto.ca ([128.100.70.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7KGAdM19453 for ; Mon, 20 Aug 2001 12:10:39 -0400 Received: from phm.utoronto.ca (lpk04.phm.utoronto.ca [128.100.70.180]) by phm.utoronto.ca (8.9.3+Sun/8.9.3) with ESMTP id MAA08648 for ; Mon, 20 Aug 2001 12:05:07 -0400 (EDT) Sender: william@phm.utoronto.ca Message-ID: <3B81362B.BAE4B2D@phm.utoronto.ca> Date: Mon, 20 Aug 2001 12:09:15 -0400 From: William Wei Reply-To: william@phm.utoronto.ca Organization: Faculty of Pharmacy, U of T X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: About amber parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Dear CCL'ers, I am a new user of amber. I have problems with developing parameters. Here is my steps: 1. Create new residue, import two residues from amber, connect them, and draw other part of the new residue. 2. Save the new residue in PDB file. Open it with sybyl, and the bonds I drawn between residues(amber) were lost. I drew it, and use mopac to caculate the charge. 3. Construct the charge, atoms type in xleap. 4. Construct the force parameters for the new residues. After these steps, I load the new residue OFF file and new force parameters, check the unit, it is okay. Then my problem was coming: while I ran xleap, load my new residue, xleap can not recognize my new atoms tpye. And while I save the residue to pdb file in leap, The sybyl can not draw it well. Does anyone have developed parameters? I really appreciate your help. Or give me some information of amber .OFF file's type. William. From chemistry-request@server.ccl.net Mon Aug 20 16:00:00 2001 Received: from unlserve.unl.edu ([129.93.1.130]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7KK00M24228 for ; Mon, 20 Aug 2001 16:00:00 -0400 Received: from localhost (rrashid@localhost) by unlserve.unl.edu (8.9.1a/8.9.2) with SMTP id PAA44726 for ; Mon, 20 Aug 2001 15:00:00 -0500 Date: Mon, 20 Aug 2001 15:00:00 -0500 (CDT) From: Ali N Rashid To: chemistry@ccl.net Subject: Transition dipoles in MOPAC. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, does anyone know how to calculate transition dipole, trasition polarizations using MOPAC 6 which is the only one I can get a hold of right now. Thanks in advance. From chemistry-request@server.ccl.net Mon Aug 20 11:59:45 2001 Received: from mail.axelero.hu ([195.228.240.10]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7KFxiM19241 for ; Mon, 20 Aug 2001 11:59:44 -0400 Received: (qmail 26782 invoked from network); 20 Aug 2001 17:59:42 +0200 Received: from line-141-192.dial.matav.net (HELO cthulhu) (145.236.141.192) by mail.axelero.hu with SMTP; 20 Aug 2001 17:59:42 +0200 Message-ID: <001101c12991$28df3cc0$0200a8c0@cthulhu> From: "Tamas Gunda" To: "Sorich, Michael Joseph - SORMJ001" , References: Subject: Re: CCL:SOMFA and CSSR file format Date: Mon, 20 Aug 2001 17:59:56 +0200 Organization: University of Debrecen MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000E_01C129A1.EBD89E00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_000E_01C129A1.EBD89E00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable SOMFA and CSSR file formatTry the page: = http://www-fbsc.ncifcrf.gov/compenv/app_soft/man/chemx/document/refindex.= htm It is the Chem-X Reference Manual Index; page down until you reach "CSSR = file format" On the other hand, could e-mail me one your files with superimposed = molecules? Mol2mol should convert them to CSSR format, I'd like to check it. Regards: Tamas E. Gunda ---------------------------- Dr Tamas E. Gunda Research Group for Antibiotics University of Debrecen H-4010 Debrecen, POBox 36 Hungary e-mail: tamasgunda@tigris.klte.hu http://dragon.klte.hu/~gundat ----- Original Message -----=20 From: Sorich, Michael Joseph - SORMJ001=20 To: 'chemistry@ccl.net'=20 Sent: Monday, August 20, 2001 6:42 AM Subject: CCL:SOMFA and CSSR file format Hello=20 I have been attempting to use SOMFA, a 3D QSAR program.=20 Superimposed molecules must be entered in CSSR (or XR) file format.=20 I have molecules aligned in the mdl SD and sybyl MOL2 formats.=20 I have used Babel, Cerius2 and Mol2Mol to convert to the CSSR=20 format. When entered into the SOMFA program, however, all these=20 converted files generate errors (eg "Error reading atom data").=20 1) Has anyone else had this problem and if so, is there a=20 solution?=20 2) Does anyone have any information on how the CSSR files=20 are formatted, so I may interpret the error messages generated.=20 Thanks for your time=20 Michael Sorich=20 PhD Student=20 University of South Australia=20 Email:SORMJ001@students.unisa.edu.au=20 or mike_sorich@hotmail.com=20 ------=_NextPart_000_000E_01C129A1.EBD89E00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable SOMFA and CSSR file format

Try the page:

http://www-fbsc.ncifcrf.gov/compenv/app_soft/man/chemx/docum= ent/refindex.htm

It is the Chem-X Reference Manual = Index; page down=20 until you reach "CSSR file format"

On the other hand, could e-mail me one = your files=20 with superimposed molecules? Mol2mol should

convert them to CSSR format, I'd like = to check=20 it.

Regards:

Tamas E. Gunda

----------------------------

Dr Tamas E. Gunda
Research Group for = Antibiotics
University of Debrecen
H-4010 Debrecen, POBox=20 36
Hungary
e-mail: tamasgunda@tigris.klte.huhttp://dragon.klte.hu/~gundat<= /FONT>

----- Original Message -----

From:=20 Sorich, Michael Joseph = -=20 SORMJ001
To: 'chemistry@ccl.net'

Sent: Monday, August 20, 2001 = 6:42=20 AM

Subject: CCL:SOMFA and CSSR = file=20 format

Hello

I have been attempting to use SOMFA, a 3D QSAR = program.=20
Superimposed molecules must be entered in = CSSR (or XR)=20 file format.
I have molecules aligned in the = mdl SD=20 and sybyl MOL2 formats.
I have used Babel, = Cerius2 and=20 Mol2Mol to convert to the CSSR
format. When = entered=20 into the SOMFA program, however, all these
converted=20 files generate errors (eg "Error reading atom data").

1) Has anyone else had this problem and if so, is = there a=20
solution?

2) Does anyone have any information on how the CSSR=20 files
are formatted, so I may interpret the = error=20 messages generated.

Thanks for your time

Michael Sorich
PhD = Student=20
University of South Australia

Email:SORMJ001@students.unisa.edu.au =
or mike_sorich@hotmail.com =

------=_NextPart_000_000E_01C129A1.EBD89E00-- From chemistry-request@server.ccl.net Mon Aug 20 19:09:35 2001 Received: from njmsa.umdnj.edu ([130.219.34.100]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7KN9ZM27916 for ; Mon, 20 Aug 2001 19:09:35 -0400 Received: from NACPC29 ([130.219.34.71]) by njmsa.umdnj.edu (8.9.3 (PHNE_18546)/8.9.3) with ESMTP id TAA15245 for ; Mon, 20 Aug 2001 19:09:34 -0400 (EDT) Date: Mon, 20 Aug 2001 19:09:32 -0400 (Eastern Daylight Time) From: Sarangian Ravichandran To: Subject: AutoDockTools (ADT) Problems Message-ID: X-Warning: UNAuthenticated Sender MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All: I have some difficulty in using AutoDockTools, ADT developed by Dr. M. Sanner. I have installed ADT in SGI(Octane2), and have been trying to redo the examples that came with AutoDock (3ptb and 1hvr sample systems) using ADT. When I read the receptor using the module AutoGpf of ADT, I am getting error messages (see below) for both 3ptb and 1hvr. I have attached only the error message for 1hvr and I get similar messages for 3ptb system. I would like to know any ADT user have experienced similar problems. Any help is greatly appreciated. regards, Ravi Email: ravichsa@umdnj.edu ------------------------------ 1hvr.pdbqs: ---------- I used AutoGpf to read the 1hvr.pdbqs file and the options I choose were to automatically merge non-polar Hs, to automatically merge lone-pairs , and save save the result as 1hvr.pdbqs non-integeral charge on 1hvr is 3.992, I hit ok and I get the following message in the python shell --------------------------------- >>> Warning: interruption in backbone between 1hvr: :PHE99:N and 1hvr: :HYD100:H of 380 Angstrom Warning: interruption in backbone between 1hvr: :HYD100:H and 1hvr: :PRO101:O of 423 Angstrom Warning: interruption in backbone between 1hvr: :PHE199:N and 1hvr: :HYD200:O of 380 Angstrom Exception in Tkinter callback Traceback (innermost last): File "/usr/people/ravi/FINALADT/share/lib/python1.5/lib-tk/Tkinter.py", line 764, in __call__ return apply(self.func, args) File "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/ AutoDockTools/autogpfCommands.py", line 761, in guiCallback mergeLPS=mergeLPS, newfilename=newfilename, checkMTypes=1, log=1, redraw=1) File "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/ ViewerFramework/VFCommand.py", line 582, in doitWrapper result = apply( self.vf.tryto, (self.func,)+args, kw ) File "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/ ViewerFramework/VF.py", line 553, in tryto result = apply( command, args, kw ) File "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/ AutoDockTools/autogpfCommands.py", line 798, in doit apply(self.vf.ADgpf_initMacro, (mol,), kw) File "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/ AutoDockTools/autogpfCommands.py", line 314, in __call__apply(self.doitWrapper,(mol,), kw) File "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/ ViewerFramework/VFCommand.py", line 582, in doitWrapper result = apply( self.vf.tryto, (self.func,)+args, kw )File "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/ ViewerFramework/VF.py", line 553, in tryto result = apply( command, args, kw ) File "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/ AutoDockTools/autogpfCommands.py", line 350, in doit if hasLPS and not mergeNPHS and not addSolPar:NameError: hasLPS ------------------------------