On 9/18/12 10:35 PM, Elie M wrote:
Dear all,
I have been reading about PRODRG that takes a PDB file as an input and produces
topologies compatible with GROMACS as an output. Can this program be then
considered as a solution to the problem of missing residues in GROMACS like LIG?
PRODRG produces topologies for the Gromos96 43a1 parameter set (and an older
version produces topologies for the outdated Gromos87), and the quality of the
topologies is generally very low. The resulting topologies require significant
modification.
N.B: I am using the OPLSAA force field .I also have the files in MDL MOL2
version which do not contain the LIG residue appearing in the PDB file. So
maybe using PRODRG on the MOL2 might solve the problem?
I don't understand this. PRODRG will be of no use here since you are using
OPLS-AA, and if there is no ligand, then why do you need some external program
to build a topology?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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 gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
