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. 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] 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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