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

Mark Abraham Mark.Abraham at anu.edu.au
Sat Nov 7 11:25:02 CET 2009

Mark Abraham wrote:
> 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 
> knowledge.

Or, you've #include some file in the wrong order - say your molecule 
.itp file before your force field files.


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