[gmx-users] Re: [ atomtypes ] are not case sensitive?
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
> I use gromacs4.0.7 and the water model is TIP4P2005.
> Q1: when I grompp the .gro( a CO2 molecular and 1240 water moleculars),
> 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
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?
Looking forward to your reply, thank you very much.
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