Dear Mark Abraham,<br><br>Thanks a lot. It helped me a lot..!!<br><br>yours sincerely,<br>Uday.<br><br><div class="gmail_quote">On Mon, Jan 24, 2011 at 2:08 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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Today's Topics:<br>
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1. Re: Gromos96 manual and user guid (Justin A. Lemkul)<br>
2. Re: PRODRG server (Justin A. Lemkul)<br>
3. pdb2gmx error_ resall.c, line: 321 (udaya kiran)<br>
4. Re: pdb2gmx error_ resall.c, line: 321 (Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 24 Jan 2011 07:27:51 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Gromos96 manual and user guid<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4D3D7047.5060907@vt.edu">4D3D7047.5060907@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
mohsen ramezanpour wrote:<br>
> Dear All<br>
> I need GROMOS96 manual and user guid for my work.<br>
> Can you send it for me?<br>
<br>
This information is (unfortunately) proprietary. You have to purchase the<br>
GROMOS software suite to obtain it.<br>
<br>
-Justin<br>
<br>
> Thanks in advance for your help.<br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 24 Jan 2011 07:31:40 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] PRODRG server<br>
To: "Gromacs Users' List" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4D3D712C.6070005@vt.edu">4D3D712C.6070005@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
mohsen ramezanpour wrote:<br>
> Dear Dr.justin<br>
> Actually by doing this we are using two different force fields in one<br>
> simulation.<br>
> I had done it before and the result was that I discussed before in<br>
> gmx-users(LINCS Error,Exploding system,Bad contacts between atoms)<br>
> Then,this approch seems to doesn't work about my system.<br>
><br>
> Then I want to find charges and charge groups for gromos 43A1 and<br>
> replace them for my drug(to edit PRODRG file manually) and work totally<br>
> in gromos 43A1.<br>
<br>
Please keep your story consistent. In the last message, you said you wanted to<br>
work completely within 53A6, so I advised you on how to do that, now you say<br>
that you're trying to work completely within 43A1.<br>
<br>
> Unfortunately I can't obtain these parameter.<br>
<br>
You certainly do have these parameters. 43A1 is part of the Gromacs<br>
installation; in the .rtp file you'll find all of the functional groups that<br>
were derived in 43A1, as applied to amino acids and a few other groups.<br>
<br>
> Please let me have if you have it.<br>
> Can I use some Ab Initio software for determining partial charges of my<br>
> drug?<br>
> for example ABINIT or Gaussian!<br>
><br>
<br>
My paper that you said you read has discussion and recommendations on this<br>
point. But be very clear: none of the QM methods we tested were able to<br>
reproduce the charges that are assigned to known functional groups since the<br>
Gromos parameterization methodology calls for "empirical refinement." Thus,<br>
manual modification and thorough validation are always necessary.<br>
<br>
-Justin<br>
<br>
> Thanks in advance<br>
><br>
> On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>> wrote:<br>
><br>
><br>
><br>
> mohsen ramezanpour wrote:<br>
><br>
> Ok<br>
> then,I can use PRODRG server to generate .top and .gro files<br>
> for drug.<br>
> since it's reported charges are not very accurate ,we can<br>
> replace all charges completely with them in 53A6(if was present).<br>
> But it means we are working in 53A6 force field.<br>
> then,we must generate .top and .gro files for our protein with<br>
> 53A6 too.<br>
> and work completely with 53A6.<br>
> Am i right?<br>
> thanks in advance<br>
><br>
><br>
> That sounds like a reasonable approach. Be sure to validate the<br>
> drug topology. In my experience, this procedure is pretty good, but<br>
> you always have to convince reviewers...<br>
><br>
> -Justin<br>
><br>
><br>
> On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul<br>
> <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>>> wrote:<br>
><br>
><br>
><br>
> mohsen ramezanpour wrote:<br>
><br>
> Dear Justin<br>
><br>
> I read your articles about PRODRG server,they were very<br>
> useful.<br>
> But I have a question:<br>
> are charges of functional groups and generally other atom<br>
> groups<br>
> the same in all force fields?<br>
> Because you have modified charges of your molecules by<br>
> Gromos96<br>
> 53A6 while prodrg server is generating topology files in<br>
> 43A1.<br>
> I want to know can I replace charges from gromos 53A6 or<br>
> other<br>
> forcefields?<br>
> thanks in advance<br>
><br>
><br>
> Charges are not the same between force fields. We did our study<br>
> with 43A1 since that is what PRODRG purports to produce. I would<br>
> say that our recommendations carry to other Gromos force<br>
> fields, as<br>
> well, but don't take charges from 43A1 and apply them to<br>
> 53A6. Be<br>
> consistent within the force field.<br>
><br>
> The atom types produced by PRODRG are largely shared between 43A1<br>
> and 53A6, so if you *completely* replace all charges with<br>
> those from<br>
> 53A6, you should have a topology that is compatible with 53A6.<br>
><br>
> -Justin<br>
><br>
> -- ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<br>
> 231-9080<br>
><br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
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> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
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--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Mon, 24 Jan 2011 13:53:19 +0100<br>
From: udaya kiran <<a href="mailto:kiran.udaya@gmail.com">kiran.udaya@gmail.com</a>><br>
Subject: [gmx-users] pdb2gmx error_ resall.c, line: 321<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<AANLkTinS0kYkOfnREV4GQdomvQWd+h1=<a href="mailto:qKAtGq4PLECm@mail.gmail.com">qKAtGq4PLECm@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear GROMACS users,<br>
<br>
I have received the following error when trying to convert a pdb file<br>
(containing N-methylated L- Leucine residue) to gro format. I am using<br>
ffG53a6 forcefield.<br>
<br>
<br>
Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat<br>
<br>
Select the Force Field:<br>
0: GROMOS96 43a1 force field<br>
1: GROMOS96 43a2 force field (improved alkane dihedrals)<br>
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)<br>
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)<br>
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>
6: [DEPRECATED] Gromacs force field (see manual)<br>
7: [DEPRECATED] Gromacs force field with hydrogens for NMR<br>
8: Encad all-atom force field, using scaled-down vacuum charges<br>
9: Encad all-atom force field, using full solvent charges<br>
4<br>
Opening library file ffG53a6.rtp<br>
Opening library file aminoacids.dat<br>
Opening library file aminoacids.dat<br>
WARNING: masses will be determined based on residue and atom names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file atommass.dat<br>
Entries in atommass.dat: 178<br>
WARNING: vdwradii will be determined based on residue and atom names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file vdwradii.dat<br>
Entries in vdwradii.dat: 28<br>
Opening library file dgsolv.dat<br>
Entries in dgsolv.dat: 7<br>
Opening library file electroneg.dat<br>
Entries in electroneg.dat: 71<br>
Opening library file elements.dat<br>
Entries in elements.dat: 218<br>
Reading 16L6_6S17_start.pdb...<br>
WARNING: all CONECT records are ignored<br>
Read '6S17 ', 39 atoms<br>
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat<br>
26 out of 26 lines of xlateat.dat converted succesfully<br>
Analyzing pdb file<br>
There are 1 chains and 0 blocks of water and 6 residues with 39 atoms<br>
<br>
chain #res #atoms<br>
1 ' ' 6 39<br>
<br>
All occupancies are one<br>
Opening library file ffG53a6.atp<br>
Atomtype 1<br>
Reading residue database... (ffG53a6)<br>
Opening library file ffG53a6.rtp<br>
Using default: not generating all possible dihedrals<br>
Using default: excluding 3 bonded neighbors<br>
Using default: generating 1,4 H--H interactions<br>
Using default: removing impropers on same bond as a proper<br>
<br>
*-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.0.5<br>
Source code file: resall.c, line: 321<br>
<br>
Fatal error:<br>
in .rtp file at line:<br>
<br>
<br>
-------------------------------------------------------<br>
*<br>
<br>
Could you please let me know what could be the problem..?<br>
<br>
yours sincerely,<br>
Uday.<br>
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<br>
Message: 4<br>
Date: Tue, 25 Jan 2011 00:08:03 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] pdb2gmx error_ resall.c, line: 321<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4D3D79B3.5040101@anu.edu.au">4D3D79B3.5040101@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 24/01/2011 11:53 PM, udaya kiran wrote:<br>
> Dear GROMACS users,<br>
><br>
> I have received the following error when trying to convert a pdb file<br>
> (containing N-methylated L- Leucine residue) to gro format. I am<br>
> using ffG53a6 forcefield.<br>
><br>
><br>
> Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat<br>
><br>
> Select the Force Field:<br>
> 0: GROMOS96 43a1 force field<br>
> 1: GROMOS96 43a2 force field (improved alkane dihedrals)<br>
> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>
> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)<br>
> 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)<br>
> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>
> 6: [DEPRECATED] Gromacs force field (see manual)<br>
> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR<br>
> 8: Encad all-atom force field, using scaled-down vacuum charges<br>
> 9: Encad all-atom force field, using full solvent charges<br>
> 4<br>
> Opening library file ffG53a6.rtp<br>
> Opening library file aminoacids.dat<br>
> Opening library file aminoacids.dat<br>
> WARNING: masses will be determined based on residue and atom names,<br>
> this can deviate from the real mass of the atom type<br>
> Opening library file atommass.dat<br>
> Entries in atommass.dat: 178<br>
> WARNING: vdwradii will be determined based on residue and atom names,<br>
> this can deviate from the real mass of the atom type<br>
> Opening library file vdwradii.dat<br>
> Entries in vdwradii.dat: 28<br>
> Opening library file dgsolv.dat<br>
> Entries in dgsolv.dat: 7<br>
> Opening library file electroneg.dat<br>
> Entries in electroneg.dat: 71<br>
> Opening library file elements.dat<br>
> Entries in elements.dat: 218<br>
> Reading 16L6_6S17_start.pdb...<br>
> WARNING: all CONECT records are ignored<br>
> Read '6S17 ', 39 atoms<br>
> Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat<br>
> 26 out of 26 lines of xlateat.dat converted succesfully<br>
> Analyzing pdb file<br>
> There are 1 chains and 0 blocks of water and 6 residues with 39 atoms<br>
><br>
> chain #res #atoms<br>
> 1 ' ' 6 39<br>
><br>
> All occupancies are one<br>
> Opening library file ffG53a6.atp<br>
> Atomtype 1<br>
> Reading residue database... (ffG53a6)<br>
> Opening library file ffG53a6.rtp<br>
> Using default: not generating all possible dihedrals<br>
> Using default: excluding 3 bonded neighbors<br>
> Using default: generating 1,4 H--H interactions<br>
> Using default: removing impropers on same bond as a proper<br>
><br>
> *-------------------------------------------------------<br>
> Program pdb2gmx, VERSION 4.0.5<br>
> Source code file: resall.c, line: 321<br>
><br>
> Fatal error:<br>
> in .rtp file at line:<br>
><br>
><br>
> -------------------------------------------------------<br>
> *<br>
><br>
> Could you please let me know what could be the problem..?<br>
<br>
You've broken the format of the .rtp file used in ffG53a6. Use the<br>
"diff" tool to compare the "before" and "after" versions. Be sure you<br>
are using unix-style line endings.<br>
<br>
Mark<br>
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