[gmx-users] Error with "grompp"

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 04:09:02 CEST 2012

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


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