[gmx-users] Error with "grompp"
elie.moujaes at hotmail.co.uk
Mon Oct 1 15:27:57 CEST 2012
Thanks for your time and help as always. I will see what I can do about that.
> 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
> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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