[gmx-users] Error with "grompp"

[Elie M]

Thanks for your time and help as always. I will see what I can do about that.
Elie

> Date: Mon, 1 Oct 2012 08:38:15 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error with "grompp"
> 
> 
> 
> On 10/1/12 12:38 AM, Elie M wrote:
> >
> > Dear all,
> > Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called "ffoplsaamod.n2t". The top file was created successfully. However when I run grompp, I get the error:
> > "Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]'"
> > I tried to "uncomment" the bond types then the error moves to contraint types. What is the solution in this case?
> > N.B: I have copied the file ffoplsaa.itp and called it "ffoplsaamod.itp".. Not sure if this has anything to do with the error.
> 
> It probably does.  The first #include statement in your topology is probably:
> 
> #include "ffoplsaa.itp"
> 
> That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp.  If you have 
> renamed the files, then ffoplsaanb.itp does not occur and cannot be #included 
> prior to ffoplsaabon.itp.  The order of inclusion is essential for proper 
> functionality.
> 
> If you need to make adjustments to the contents of any of these files, make a 
> local copy of the entire force field and make modifications, leaving the files 
> located in $GMXLIB alone.  Do not rename them unless you consistently rename all 
> references to these files.
> 
> -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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