Sorry one more thing: For one of the atoms S that x2top did not assign the topology it said 0 bonds although S is a part of the Thiophene molecule which is connected to two carbons..what does it mean "0 bonds"?
Thanks > From: [email protected] > To: [email protected] > Subject: RE: [gmx-users] error with x2top. > Date: Tue, 25 Sep 2012 22:17:21 +0100 > > > 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: [email protected] > > To: [email protected] > > 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 [email protected] > > 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 [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
