[gmx-users] Error with "grompp"

[Elie M]

I guess now I get what is happening finally. Correct me if I am wrong.  The .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which was also modified to include atoms that were not there *but present in atomtypes.atp). The .top file describes all the bonds and angles in the molecule. This was successful. However the characteristics of some of those bonds are not described in the foplssabon.itp file; for example I have Sulfur in my molecule connected to carbon which has no entry in foplsaabon.itp and must be added to that file manually. I guess now I am in a position to check those bonds and add the relevant information which i will gather maybe from HYPERCHEM or ARGUSLAB??....A final question is in order here:
what do the parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and in what units?

Thank you very much
Elie  

> Date: Thu, 4 Oct 2012 12:25:48 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error with "grompp"
> 
> 
> 
> On 10/4/12 12:13 PM, Elie M wrote:
> >
> > Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; I have commented ";" one line which was given the first two errors. Now the only errors remaining are the bonds, angles and some others. How to correct these?
> > For example one of them is (the error occuring at line 118 which is no different from others).
> >   111  [ bonds ]   112  ;  ai    aj funct            c0            c1            c2            c3   113      1     2     1   114      1     5     1   115      1    47     1   116      2     3     1   117      2    48     1   118      3     4     1
> >   How can the source of error be known and corrected?
> 
> The error message means that no suitable parameters exist in the force field for 
> the bond that occurs between those atoms.  You either need to parameterize the 
> problematic bond(s) yourself or obtain parameters from some other reliable source.
> 
> -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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