Yep You are right. I will try my best to change the files accordingly. Thanks
> Date: Tue, 25 Sep 2012 17:05:20 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] error with x2top. > > > > On 9/25/12 5:02 PM, Elie M wrote: > > > > Thanks for your reply. I guess either way (x2top or pdb2gmx), I have > > problems. pdb2gmx is giving the same old error residue 'UNK' is not found > > in topology residue file whereas strangely enough x2top did not complain > > and was able to assign topologies for 73 atoms out of 94 so maybe it is > > easier to use x2top because in the other case I have to change files and I > > have no experience in this whatsoever and I am really tight on time. What > > do you personally think? > > > > Neither tool is guaranteed to produce a topology for an arbitrary molecule. > If > g_x2top does not have the right parameters, it will fail. If pdb2gmx does > not > have the right parameters, it will fail. g_x2top further assumes that some > generic set of atom types and functional groups will address whatever it is > that > you're working with. Sometimes that's appropriate, sometimes it's not. > Either > way, you're going to have to modify either the .n2t file or the .rtp file for > your chosen force field. Regardless of the route you choose, you're going to > have to come up with parameters for your molecule and learn how these files > work > so you can modify them. Parameterization is an expert topic for a reason. > > -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
