> 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?
- The "LIG" residue only appears in the pdb version of the file. I tried to use editconf on the .mol type of file to change into .gro file but it gave an error so I thought editconf only changes pdb files into .gro ones. This raises a question: What other types of files does editconf change into .gro? Anyways, this is a part of the .mol file produced by Marvin Sketch: Mrv0541 09081217542D 46 50 0 0 0 0 999 V2000 5.3375 -1.9029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7500 -2.6174 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1979 -3.2305 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 4.4443 -2.8949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5305 -2.0744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0153 -2.8949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7298 -3.3074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7298 -4.1324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0153 -4.5449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3008 -4.1324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3008 -3.3074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8327 -4.2093 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0.......... Thanks for your help Elie > Date: Wed, 19 Sep 2012 05:23:28 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] use of PRODRG > > > > 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 version produces topologies for the outdated Gromos87), and the quality of 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 -- 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
