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? 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
