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

[Mark Abraham]

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.

Mark

>      my co2.itp is following:
> [ atomtypes ]
>
> ;   type      mass    charge    ptype    sigma       epsilon
>
>         C  12.01100    0.5888       A     0.27918    0.239832
>
>         O  15.99940   -0.2944       A     0.30000    0.687244
>
>
> [ moleculetype ]
>
> ; molname	nrexcl
>
> CO2		2
>
>
> [ atoms ]
>
> ;   nr   type  resnr residue  atom   cgnr     charge       mass
>
>       1	    C	   1	CO2      C      1     0.5888
>
>       2	    O	   1	CO2    OC1      1    -0.2944
>
>       3	    O	   1	CO2    OC2      1    -0.2944
>
>
>
> #ifdef FLEXIBLE
>
> [ bonds ]
>
> ; i     j       funct   length  force.c.
>
> 1       2       1       0.1163  345000.0 0.1163        345000.0
>
> 1       3       1       0.1163  345000.0 0.1163        345000.0
>
>
> [ angles ]
>
> ; i	j	k	funct	angle	force.c.
>
> 2	1	3	1	180.00	383	180.00	383
>
>
> #else
>
> [ settles ]
>
> ; C	funct	dco	doo
>
> 1	1	0.1163	0.2326
>
>
> [ exclusions ]
>
> 1	2	3
>
> 2	1	3
>
> 3	1	2
>
> #endif
>
> Looking forward to your reply, thank you  very much.
>   
>
>
>
>
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/atomtypes-are-not-case-sensitive-tp4426581p4999917.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.