[gmx-users] Re: minimizing ligand only

Anna Marabotti anna.marabotti at isa.cnr.it
Tue May 18 10:28:32 CEST 2010

Dear Justin,
thank you for your answer. Actually I did the changes that you suggest, but
the problem seems to be the fact that I called "lig" my molecule. In fact,
the error message told that "The moleculetype lig is redefined". When I
changed its name, it seemed to work. Is there some problem in GROMACS if I
use "lig" to name a molecule?
Another question: if I start directly from the ligand, I cannot start the
minimization, I am forced to start from editconf to create an empty box
because GROMACS complains that the values for cut-off are larger than box
dimensions. So, to minimize a molecule, do I have at least to insert it into
a box, even if I don't want to add water? It's not a problem for me to do
it, it's only to know what is the proper procedure to minimize in vacuo a
small ligand.

Thanks again and regards

Message: 3
Date: Mon, 17 May 2010 12:30:17 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] minimizing ligand only
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4BF16F19.5000409 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Anna Marabotti wrote:
> Dear gmx-users,
> is it possible to minimize a ligand in vacuo, not inserted in a protein, 
> using GROMACS? I tried to do it using the topology file created by 
> PRODRG server and skipping the pdb2gmx, editconf, genbox steps, but 
> GROMACS gave me an error indicating that it does not recognize the 
> moleculetype. The command I used was:
> grompp -f em.mdp -c lig.pdb -o ligmin.tpr -o ligtopol_by_PRODRG.top
> I made two attempts: first, I used the .itp file directly coming from 
> PRODRG, second, I modified this file by adding the missing infos on my 
> ligand under the different parts [ molecules ], [ systems] and so on. 
> But I was not able to force Gromacs recognizing my molecule. Obviously, 
> my ligand is not a peptide, but is a small molecule.
> I searched for some hints in the gmx-users archive and found this message:
> http://lists.gromacs.org/pipermail/gmx-users/2008-October/037164.html
> but it seems to me that it does not answer to my problem. If I follow 
> the Kerrigan's tutorial, it indicates how to create a topology for the 
> ligand, but not how to minimize it in the absence of the protein.
> Could you give me a more clear explanation? Sorry if the request seems 
> to be trivial, but I really can't understand what to do.

You just need to create a proper .top file from the .itp file.  There is
little to do in order to make this change:


If you need further help, please post the actual error message and your 
topology.  On a separate note, if you're using an unedited PRODRG topology,
charges and charge groups (at face value) are often unsatisfactory, so do 
proceed carefully...


> Many thanks in advance and best regards
> Anna
> __________________________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabotti at isa.cnr.it <mailto:amarabotti at isa.cnr.it>
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
> "If you think you're too small to make a change, try sleeping with a 
> mosquito"


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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