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" <[email protected]> Subject: Re: [gmx-users] minimizing ligand only To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> 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: [email protected] <mailto:[email protected]> > 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 MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
