[gmx-users] Error with "grompp"
elie.moujaes at hotmail.co.uk
Thu Oct 4 16:12:25 CEST 2012
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
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?
> Date: Wed, 3 Oct 2012 22:09:02 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error with "grompp"
> On 10/3/12 7:48 PM, Elie M wrote:
> > Sorry it seems that those breaks are due to hotmail and not present in the topology. Thanks for your reply. I still have problems...I will tell u briefly and as clear as possible what i did.
> > (1) My top file has the following lines ate first:
> > ; Include forcefield parameters #include "ffoplsaamod.itp"[ moleculetype ]
> > which means that when grompp is reading it, it will first go to ffoplsaamod.itp.
> > (2) After the description of what the ffoplsaamod is (commented by ";"), the input is simply:
> > [ defaults ];nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 3 yes 0.5 0.5
> > #include "ffoplsaanb.itp"#include "ffoplsaabon.itp"
> > where the nonbonded and bonded parameters are included in this order (which you have also mentioned in your previous e-mail). If i run grompp in this way I get the error:
> > Fatal error:Syntax error - File ffoplsaamod.itp, line 18Last line read:'\par'Found a second defaults directive.
> > which I really cannot understand. The above [defaults] is the first thing that the code will pass through. How come it mentions this as a second directory?
> > (3) i commented the above [ defaults] with a ";" and I get another error:
> > Fatal error:Syntax error - File ffoplsaanb.itp, line 1Last line read:'[ atomtypes ]'Invalid order for directive atomtypes
> > which might mean according to what I have read (correct me if I am wrong please), that the order might be violated and that [atomtypes] should not come first; but it is the first directive in the ffoplsaanb.itp file, which should be read first.
> > So what might be happening? what is going wrong? or maybe what am I missing?Thank you all once again for the effort you are making in this forum
> It seems like the format of whatever files you're using is horribly broken. I
> would recommend starting over and not making any adjustments to any files
> (removing lines, changing contents, adding comments, etc) unless you know
> exactly what you're doing. For example, the presence of '\par' in
> ffoplsaamod.itp suggests wrong line endings (i.e. from not using a plain text
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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