[gmx-users] Re: [ atomtypes ] are not case sensitive?
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
>> 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
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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