[gmx-users] minimizing ligand only

Anna Marabotti anna.marabotti at isa.cnr.it
Mon May 17 12:13:31 CEST 2010

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:
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 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
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
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