<div class="gmail_quote"><div><div>Hello Justin, thank you for answering!</div><div>I think I already have done what you suggested when I created my</div><div>ffbonded.itp and .rtp files.</div><div><br></div><div>I am sending a piece of my topology and ffbonded.itp files.</div>
<div>Follows also the residue from .rtp and the configuration of glycol (.gro) </div><div>so you can consider where I might be wrong and what I still must do.</div><div>Thanks again.</div><div><br></div><div>eef </div><div>
<br></div><div><br></div><div>!!! topol.top !!!</div><div>; Include forcefield parameters</div><div>#include "charmm27.ff/forcefield.itp"</div><div><br></div><div>[ moleculetype ]</div><div>; Name nrexcl</div>
<div>Other 3</div><div><br></div><div>[ atoms ]</div><div>; nr type resnr residue atom cgnr charge mass typeB chargeB massB</div><div> 1 HCP1 1 PA2 HOA 1 0.42 1.008 ; qtot 0.42</div>
<div> 2 OC311 1 PA2 OHA 1 -0.65 15.9994 ; qtot -0.23</div><div> 3 CC322 1 PA2 CA 1 0.05 12.011 ; qtot -0.18</div><div> 4 HCA2 1 PA2 HA1 1 0.09 1.008 ; qtot -0.09</div>
<div> ...</div><div> </div><div>[ bonds ]</div><div>; ai aj funct c0 c1 c2 c3</div><div> 1 2 1 </div><div> 2 3 1 </div><div> 3 4 1 </div>
<div> ...</div><div> </div><div>[ pairs ]</div><div>; ai aj funct c0 c1 c2 c3</div><div> 1 4 1 </div><div> 1 5 1 </div><div> 1 6 1 </div>
<div> ...</div><div> </div><div>[ angles ]</div><div>; ai aj ak funct c0 c1 c2 c3</div><div> 1 2 3 5 </div><div> 2 3 4 5 </div><div> ...</div>
<div> </div><div>[ dihedrals ]</div><div>; ai aj ak al funct c0 c1 c2 c3 c4 c5</div><div> 1 2 3 4 9 </div><div> ...</div><div>
</div><div><br></div><div>!!! ffbonded.itp !!!</div><div>[ bondtypes ]</div><div>; i j func b0 kb</div><div>OC311 HCP1 1 0.0960 456056.0 ; par22 OH1 H</div><div>CC322 OC311 1 0.1420 334720.0 ; adm 11/08, glycerol</div>
<div>CC322 HCA2 1 0.1111 258571.2 ; par22 HA CT2</div><div>[ angletypes ]</div><div>; i j k func th0 cth ub0 cub</div><div>HCP1 OC311 CC312 5 106.00 412.40 0.0 0.00 ; og 1/06 EtOH IR fit</div>
<div>[ dihedraltypes ]</div><div>; i j k l func phi0 cp mult</div><div>HCP1 OC311 CC322 HCA2 9 0.0 0.75 3 ; og methanol</div><div><br></div><div>!!! file.rtp !!!</div>
<div><br></div><div>[ PA2 ]</div><div>; Glycol</div><div> [ atoms ]</div><div> HOA HCP1 0.420 1</div><div> OHA OC311 -0.650 1</div><div> CA CC322 0.050 1</div><div> HA1 HCA2 0.090 1</div>
<div> HA2 HCA2 0.090 1</div><div> CB CC322 0.050 2</div><div> HB1 HCA2 0.090 2</div><div> HB2 HCA2 0.090 2</div><div> OHB OC311 -0.650 2</div><div> HOB HCP1 0.420 2</div>
<div><br></div><div> [ bonds ]</div><div> OHA HOA</div><div> OHA CA</div><div> CA HA1</div><div> CA HA2</div><div> CB CA</div><div> CB HB1</div><div> CB HB2</div><div> OHB CB</div><div>
HOB OHB</div><div><br></div><div>!!! conf.gro !!!</div><div>GROningen MAchine for Chemical Simulation</div><div> 10</div><div> 1PA2 HOA 1 -0.248 -0.048 0.000</div><div> 1PA2 OHA 2 -0.177 0.017 0.000</div>
<div> 1PA2 CA 3 -0.052 -0.052 0.000</div><div> 1PA2 HA1 4 -0.041 -0.115 0.089</div><div> 1PA2 HA2 5 -0.041 -0.115 -0.089</div><div> 1PA2 CB 6 0.057 0.054 0.000</div><div>
1PA2 HB1 7 0.046 0.117 -0.089</div><div> 1PA2 HB2 8 0.046 0.117 0.089</div><div> 1PA2 OHB 9 0.182 -0.015 0.000</div><div> 1PA2 HOB 10 0.253 0.049 0.000</div><div> 3.00000 3.00000 3.00000</div>
<div><br></div><div><br></div><div>_______________________________________</div><div>Eudes Eterno Fileti</div><div>Centro de Ciências Naturais e Humanas</div><div>Universidade Federal do ABC — CCNH</div><div>Av. dos Estados, 5001</div>
<div>Santo André - SP - Brasil</div><div>CEP 09210-971</div><div>+55.11.4996-0196</div><div><a href="http://fileti.ufabc.edu.br">http://fileti.ufabc.edu.br</a></div><div><br></div></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername"></b> <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>></span><br>
Date: Mon, Aug 23, 2010 at 7:00 AM<br>Subject: gmx-users Digest, Vol 76, Issue 113<br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><br><br>Send gmx-users mailing list submissions to<br>
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Today's Topics:<br>
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1. Metallic boundary conditions (<a href="mailto:pojeda@icp.uni-stuttgart.de" target="_blank">pojeda@icp.uni-stuttgart.de</a>)<br>
2. Charmm to Gromacs: Polyols force field (Eudes Fileti)<br>
3. Re: Charmm to Gromacs: Polyols force field (Justin A. Lemkul)<br>
4. PMF (abdul wadood)<br>
5. Re: please, how edr data is xdr packed? (Sander Pronk)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sun, 22 Aug 2010 17:52:46 +0200<br>
From: <a href="mailto:pojeda@icp.uni-stuttgart.de" target="_blank">pojeda@icp.uni-stuttgart.de</a><br>
Subject: [gmx-users] Metallic boundary conditions<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:3e5fe7757a687609503cad715e2a5d15.squirrel@www.icp.uni-stuttgart.de" target="_blank">3e5fe7757a687609503cad715e2a5d15.squirrel@www.icp.uni-stuttgart.de</a>><br>
Content-Type: text/plain;charset=iso-8859-1<br>
<br>
<br>
Hi,<br>
<br>
thank you for your answer. What is then epsilon_r ?<br>
<br>
regards.<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Sun, 22 Aug 2010 14:42:43 -0300<br>
From: Eudes Fileti <<a href="mailto:fileti@ufabc.edu.br" target="_blank">fileti@ufabc.edu.br</a>><br>
Subject: [gmx-users] Charmm to Gromacs: Polyols force field<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:AANLkTikQtLsHdgQsMprykc0X0fjiQ%2BC_ydzcM6pKE5OV@mail.gmail.com" target="_blank">AANLkTikQtLsHdgQsMprykc0X0fjiQ+C_ydzcM6pKE5OV@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Olá pessoal,<br>
<br>
Recently, McKerrel published his CHARMM force field to polyols (JCTC, 2009,<br>
5, 1315).<br>
I am very interested in using it in GROMACS.<br>
<br>
For this, I began the transfer of the parameters with the following recipe:<br>
<br>
1) All atom types were added to the atomtypes.atp file;<br>
2) All bonded parameters (bonds, angles, ub, dihedral and impropers)<br>
were added to the ffbonded.itp file;<br>
3) van der Waals and Coulomb parameters were inserted properly<br>
in ffnonbonded.itp;<br>
4) The residues were created in a new file named polyols.rtp.<br>
<br>
Well, pdb2gmx works fine! It generates the restraints file (posre.itp),<br>
configuration file<br>
(conf.gro) and topology file (topol.itp). But when I run it in grommp, the<br>
default for<br>
parameters are not found. Something like:<br>
<br>
ERROR 6 [file topol.top, line 40]:<br>
No default Bond types<br>
<br>
I know I can insert the parameters by hand in each .top file generated by<br>
pdb2gmx.<br>
But what I need to do, so that grompp recognizes the default values<br>
automatically.<br>
<br>
Did I forgot some file? I'm making some mistake?<br>
<br>
Any suggestion is welcome!<br>
<br>
Muito obrigado!<br>
eef<br>
<br>
_______________________________________<br>
Eudes Eterno Fileti<br>
Centro de Ciências Naturais e Humanas<br>
Universidade Federal do ABC — CCNH<br>
Av. dos Estados, 5001<br>
Santo André - SP - Brasil<br>
CEP 09210-971<br>
+55.11.4996-0196<br>
<a href="http://fileti.ufabc.edu.br" target="_blank">http://fileti.ufabc.edu.br</a><br>
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Message: 3<br>
Date: Sun, 22 Aug 2010 13:46:39 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Charmm to Gromacs: Polyols force field<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4C71627F.1000402@vt.edu" target="_blank">4C71627F.1000402@vt.edu</a>><br>
Content-Type: text/plain; charset=windows-1252; format=flowed<br>
<br>
<br>
<br>
Eudes Fileti wrote:<br>
> Olá pessoal,<br>
><br>
> Recently, McKerrel published his CHARMM force field to polyols (JCTC,<br>
> 2009, 5, 1315).<br>
> I am very interested in using it in GROMACS.<br>
><br>
> For this, I began the transfer of the parameters with the following recipe:<br>
><br>
> 1) All atom types were added to the atomtypes.atp file;<br>
> 2) All bonded parameters (bonds, angles, ub, dihedral and impropers)<br>
> were added to the ffbonded.itp file;<br>
> 3) van der Waals and Coulomb parameters were inserted properly<br>
> in ffnonbonded.itp;<br>
> 4) The residues were created in a new file named polyols.rtp.<br>
><br>
> Well, pdb2gmx works fine! It generates the restraints file (posre.itp),<br>
> configuration file<br>
> (conf.gro) and topology file (topol.itp). But when I run it in grommp,<br>
> the default for<br>
> parameters are not found. Something like:<br>
><br>
> ERROR 6 [file topol.top, line 40]:<br>
> No default Bond types<br>
><br>
> I know I can insert the parameters by hand in each .top file generated<br>
> by pdb2gmx.<br>
> But what I need to do, so that grompp recognizes the default values<br>
> automatically.<br>
><br>
> Did I forgot some file? I'm making some mistake?<br>
><br>
<br>
Look on line 40 of the topology and see which atoms grompp is complaining about.<br>
You likely forgot to define the parameters for that particular bond type.<br>
<br>
-Justin<br>
<br>
> Any suggestion is welcome!<br>
><br>
> Muito obrigado!<br>
> eef<br>
><br>
> _______________________________________<br>
> Eudes Eterno Fileti<br>
> Centro de Ciências Naturais e Humanas<br>
> Universidade Federal do ABC — CCNH<br>
> Av. dos Estados, 5001<br>
> Santo André - SP - Brasil<br>
> CEP 09210-971<br>
> +55.11.4996-0196<br>
> <a href="http://fileti.ufabc.edu.br" target="_blank">http://fileti.ufabc.edu.br</a><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: 4<br>
Date: Mon, 23 Aug 2010 06:23:39 +0000<br>
From: abdul wadood <<a href="mailto:wadoodbiochemist@hotmail.com" target="_blank">wadoodbiochemist@hotmail.com</a>><br>
Subject: [gmx-users] PMF<br>
To: gromacs <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <BAY121-W7C84BC40D94BEBF163356D0820@phx.gbl><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
<br>
Hi, All<br>
<br>
I am trying to calculate pmf for enzyme ligand complex using the tutorial of umbrella sampling.<br>
I have successfully created the unit cell around the protein and have solvated. The ions were also added by genion.<br>
But when I run the minimization step with the command<br>
grompp -f minim.mdp -c solv_ions.gro -p 3JY0.top -o em.tpr<br>
the following error comes<br>
<br>
<br>
Fatal error:<br>
Molecule type 'NA+' contains no atoms<br>
<br>
<br>
I tried my best to solve the problem but could no succeeded.<br>
Any help to solve this problem will be highly appreciated.<br>
The topology file is attached.<br>
<br>
Thanks in advace<br>
<br>
Many regards<br>
<br>
Abdul Wadood,<br>
Research Scholar,<br>
Dr.Panjwani Center for Molecular Medicine and<br>
Drug Research,<br>
International Center for Chemical and<br>
Biological Science,<br>
University of Karachi, Karachi-75720, Pakistan.<br>
<a href="mailto:Email%3Awadoodbiochemist@hotmail.com" target="_blank">Email:wadoodbiochemist@hotmail.com</a><br>
<br>
<br>
<br>
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Message: 5<br>
Date: Mon, 23 Aug 2010 09:56:26 +0200<br>
From: Sander Pronk <<a href="mailto:pronk@cbr.su.se" target="_blank">pronk@cbr.su.se</a>><br>
Subject: Re: [gmx-users] please, how edr data is xdr packed?<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:31D44996-834B-4F78-8880-81320FE9E651@cbr.su.se" target="_blank">31D44996-834B-4F78-8880-81320FE9E651@cbr.su.se</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
As David said, the reading/writing is done in src/gmxlib/enxio.c, but you could also read edr files indirectly through gmxdump: that should also give you an idea of the type of information in those files.<br>
<br>
<br>
<br>
On Aug 22, 2010, at 13:14 , Alan Wilter Sousa da Silva wrote:<br>
<br>
> Hi there,<br>
><br>
> I am trying to use python xdrlib module to read edr files but not knowing how the data is packed using the xdr protocol makes my work very difficult, if not impossible.<br>
><br>
> Would someone kindly tell me how data is packed in the edr file? Or where it is the gromacs code so I can try to figure out a way?<br>
><br>
> I've read <a href="http://tools.ietf.org/html/rfc1832.html" target="_blank">http://tools.ietf.org/html/rfc1832.html</a> and for reference, see topic "6. AN EXAMPLE OF AN XDR DATA DESCRIPTION".<br>
><br>
> My other option would be using a parsing code to read g_energy output but this seems very silly.<br>
><br>
> Many thanks in advance,<br>
><br>
> Alan<br>
><br>
> --<br>
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
> Department of Biochemistry, University of Cambridge.<br>
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
> >><a href="http://www.bio.cam.ac.uk/~awd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
> --<br>
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