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

juanjuan0618 chanjuan0618 at 126.com
Sat Aug 4 16:31:38 CEST 2012

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.

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