[gmx-users] Re: minimizing ligand only

Thomas Schlesier schlesi at uni-mainz.de
Tue May 18 12:43:58 CEST 2010

To the second question:
PRODRG makes usually a very small box (sometimes smaller then the 
molecule, if i remember correctly), so if you want to use periodic 
boundary conditions you must make the box large enough, so that there 
are no problems with cut-offs.
The easiest way to make the minimisation in vaccuo would be that you set 
'pbc=no' (then you have no problems with the box size). I think with 
'pbc=no' you will also need 'ns_type=simple'. Then since you will have 
only few particals you can also disable the cut-offs entirely (set them 
all to zero).


> Message: 1
> Date: Tue, 18 May 2010 10:28:32 +0200
> From: Anna Marabotti <anna.marabotti at isa.cnr.it>
> Subject: [gmx-users] Re: minimizing ligand only
> To: gmx-users at gromacs.org
> Message-ID: <9609D6A92B3D4297941ED608B4E2638F at AnnaNetbook>
> Content-Type: text/plain; charset=us-ascii
> 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
> Anna
> 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
> very 
> little to do in order to make this change:
> http://www.gromacs.org/Documentation/File_Formats/.itp_File
> 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,
> the 
> charges and charge groups (at face value) are often unsatisfactory, so do 
> proceed carefully...
> -Justin
>> 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"

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