[gmx-users] Problem with simulation of aromatic structures in methanol

Mark Abraham Mark.Abraham at anu.edu.au
Sat Nov 7 11:20:54 CET 2009

radhika jaswal wrote:
> Respected Sir,
> I have problm with simulation of aromatic structures in methanol...the 
> error which comes is like...
> checking input for internal consistency...
> calling /usr/bin/cpp...
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter combinations
> Cleaning up temporary file gromppu2ZcH8
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: topio.c, line: 388
> Fatal error:
> Invalid order for directive atomtypes, file ""methanol.itp"", line 3
> -------------------------------------------------------
> I have checked all the files...and the program runs fine for aliphatic 
> structures....

The error message is quite specific - you can't have two atomtypes 
directives. Probably, you're #including parts of two force field files, 
which is not allowed, and probably a bad idea if you're mixing two 
distinct force fields. Go and find where you're getting more than one 
atomtypes and re-think. Re-read chapter 5 of the manual if you need more 


> Please tell me the point where i am making a mistake...
> With Regards
> Radhika
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