[gmx-users] Re: [ atomtypes ] are not case sensitive?

Justin Lemkul jalemkul at vt.edu
Sat Aug 4 16:34:08 CEST 2012

On 8/4/12 10:31 AM, juanjuan0618 wrote:
> On 1/08/2012 11:29 PM, juanjuan0618 wrote:
>> Dear professor,
>> Now I want to simulate the water and carbon dioxide mixture solution,but
>> when I do the simulation with my own .gro and .itp files, I  met some
>> questions.
>> I use gromacs4.0.7 and the water model is TIP4P2005.
>> Q1: when I grompp the .gro( a CO2 molecular and 1240 water moleculars),
>> .top
>> and .mdp files, it prompts me
>>         WARNING 1  [file co2.itp, line 3]:
>>                  Overriding atomtype C
>>         WARNING 2  [file co2.itp, line 4]:
>>                  Overriding atomtype O
>>          how can I remove these warning?
> Define them with unique names if they should be distinct, or don't
> redefine them if they should be the same as the ones in the force field.
>> Q2: when I grompp the other .gro with a water cage(20 water moleculars)
>> containing a CO2 molecular  and 1240 water moleculars, it prompts me
>>          Syntax error - File co2.itp, line 1
>>          Last line read:
>>          '[ atomtypes ]'
>>          Invalid order for directive atomtypes
>>          Can you tell me how I could remove this error?
> You've probably got some bizarre line ending or non-text formatting.
> Plain text, preferably with unix-style line endings, will work. dos2unix
> tool may be your friend.
> Thank you very much for your answers, Question 1 has been solved, but the
> second question is still appearing. I try to change the file style to unix
> by using dos2unix, but the problem isn't solved.
> When I change the order of the including file of the topology file, it may
> prompts me
>   Syntax error - File tip4p.itp, line 4
>            Last line read:
>            '[ moleculetype ]'
>            Invalid order for directive moleculetype
> or  prommpt me
>          Syntax error - File co2.itp, line 1
>           Last line read:
>           '[ atomtypes ]'
>           Invalid order for directive atomtypes
>           I can't find what's error, and I don't know how to solve the
> problem. Can you tell me what  could I to remove this error?
> http://gromacs.5086.n6.nabble.com/file/n4999956/co2.itp co2.itp
> http://gromacs.5086.n6.nabble.com/file/n4999956/co2-01-00.top co2-01-00.top
>   Looking forward to your reply, thank you  very much.

There is an order in which directives are allowed to appear.  Refer to Chapter 5 
of the manual.  All directives at the force field level ([defaults], 
[atomtypes], etc) must come before any [moleculetype] can be declared.  If 
you're moving around #include statements, you're probably breaking the required 



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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