Hey Justin, Thanks for the help. There is a ligand in my system, whose top file comes from the PRODRG package. PRODRG package only gives the ffgmx force field. Could ffgmx ligand combine protein with other force field? I would be happy to transfer to the newer force field if my system allows. Thanks again and have a good weekend!
Tanping --- On Fri, 2/17/12, Justin A. Lemkul <jalem...@vt.edu> wrote: > From: Justin A. Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] The solvation free energy of a vdw ligand > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Friday, February 17, 2012, 1:38 PM > > > Tanping Li wrote: > > Hey Justin, > > > > Thanks for the help. I've generated big size of data so > I hope I can find the way to fix the problem before transfer > to the new version. > > > > I just find that it gives me problem when I use the > self-defined atom type in the state B, however works fine if > I use the existing atom type in the state B. > > > > I defined the atom types by the following way: > > > > [ atometypes ] > > ;name mass > charge Ptype C6 C12 > > dum_CH3 15.035 > 0 A > 0 0 > > .... > > .... > > > > > > Did I missed some there? I noticed that the "at. num" > is included in the ffgmxnb.itp file. I searched the manual, > but haven't find that. > > > > It's the atomic number. Different force fields have > their lines parsed differently, unfortunately, so you have > to adhere to the existing format. Add a zero in the > column for atom number and see if this improves the > situation. I would recommend not using ffgmx for > anything, though. The newer manual gives several > reasons why it's a bad choice for just about any modern > simulation. > > -Justin > > -- ======================================== > > 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 > > ======================================== > -- 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
