[gmx-users] Error with "grompp"

[Elie M]

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: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> 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: jalemkul at vt.edu
> >> To: gmx-users at gromacs.org
> >> 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
> >>
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> -- 
> ========================================
> 
> 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
> 
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