[gmx-users] Error with "grompp"
elie.moujaes at hotmail.co.uk
Thu Oct 4 18:13:32 CEST 2012
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?
> Date: Thu, 4 Oct 2012 10:26:04 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error with "grompp"
> On 10/4/12 10:12 AM, Elie M wrote:
> > Hello everyone,
> > Justin, I have repeated the procedures without doing any changes and it does seem that you were right about the broken file. However now I get a different set of errors:
> > (1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
> > (2) ERROR 2 [file ffoplsaabon.itp, line 2694]: Not enough parameters
> You should inspect ffoplsaabon.itp to see what is on these lines. It is odd
> that grompp would complain about standard force field files if they have not
> been changed.
> > and then a lot of errors of the type:
> > ERROR 3 [file S54.top, line 118]: No default Bond types
> > ERROR 4 [file S54.top, line 120]: No default Bond types
> > ERROR 5 [file S54.top, line 124]: No default Bond types
> > ERROR 6 [file S54.top, line 127]: No default Bond types.......
> > Maybe the main question is for the third error is how to define these bond types and angles?
> If a certain interaction is not available in ffbonded.itp (i.e. you've got bonds
> that are not parameterized in the chosen force field) you need to add them
> either in ffbonded.itp (potentially dangerous, given the previous posts) or
> directly in the topology (probably safer).
> 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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