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
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