Yeah sorry about that. i thought about it at the moment I was sending the e-mail..The problem I am so desperate about getting all files correct to minimize my polymer. It has really taken a long time. Anyhow you were right. Switching the order did not do anything; the error is still there. Now it is a bit weird because the bond is there in the file then why it cannot find it? Any suggestions?
Elie > Date: Sat, 6 Oct 2012 13:59:10 -0400 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/6/12 1:57 PM, Elie M wrote: > > > > Yes I just saw that. thanks for turning my attention. The top file assigned > > this order of the atoms....do you think switching the order of the atoms in > > the top file would solve the problem? > > In principle, I don't think it should matter, but it's something you can > check > yourself in less time than it takes to send an email :) > > -Justin > > > Elie > > > >> Date: Sat, 6 Oct 2012 13:26:38 -0400 > >> From: [email protected] > >> To: [email protected] > >> Subject: Re: [gmx-users] Error with "grompp" > >> > >> > >> > >> On 10/6/12 1:18 PM, Elie M wrote: > >>> > >>> This is what I did. For example one of the [bonds] problems is a bond > >>> between S and one of the carbons C in the thiophene molecule. In the n2t > >>> file. I have added OPLSA_734 S because it si related to " all-atom S: > >>> thiophenol (HS is #204)"; the corresponding C was assigned an OPLSA_735 I > >>> have looked for the symbols for these two: the first is SH and the other > >>> is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: > >>> SH CA 1 0.15925 186649.5 ; > >>> However the error related to this bond is still present. I was just > >>> thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen > >>> because the symbol is SH?? maybe this is the source of the error and I > >>> have to redefine things in the .n2t file? > >>> > >> > >> It may be a matter of the order of the atoms. SH is indeed sulfur (you > >> can tell > >> by the mass in atomtypes.atp and the fact that the first letter is S). The > >> corresponding H atom is HS, so that's not the problem. The parameters for > >> this > >> bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a > >> pre-4.5 > >> version): > >> > >> CA SH 1 0.17400 209200.0 ; wlj > >> > >> -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 > > > > -- > ======================================== > > 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
