[gmx-users] error with indexfile

[Justin Lemkul]

On 1/4/13 5:06 AM, Kieu Thu Nguyen wrote:
> Thank Neha ! I follow your advices but this error still appear. I don't
> know why.
>

You'll have to show us exactly what you're doing to get any solid advice. 
Consider what I posted earlier.  Usually the mismatch occurs because you are 
using a coordinate file from some prior step in building your system that no 
longer matches the actual system.

> By the way, does anybody know why there are not ions in topology file in
> Martini CG-MD. Because I see the system has not zero charge, i don't
> understand why the CG system not be neutralized by ions.
>

There are ion parameters for MARTINI:

http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters/60-ions

-Justin

> Thanks and regards,
> KT
>
>
> On Fri, Jan 4, 2013 at 3:40 PM, Awasthi, Neha <
> neha.awasthi at biologie.uni-goettingen.de> wrote:
>
>> First check your .gro file and your .top file, to make sure atom 6518 (or
>> Water) is consistently defined.
>>
>> Next step would be to make sure this atom features in the index file
>> within a
>> "correct group".
>> In some cases, if a single atom is left out and not part of any group in
>> the
>> index file, it gives this error.
>> Why not make your index file again ?
>> Read the help provided with the command "make_ndx" to understand this.
>> Hope that works!
>>
>> -----Original Message-----
>> From: gmx-users-bounces at gromacs.org on behalf of Kieu Thu Nguyen
>> Sent: Fri 1/4/2013 6:51 AM
>> To: Discussion list for GROMACS users
>> Subject: [gmx-users] error with indexfile
>>   Dear All,
>>
>> When using the command
>> grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o
>> equilibrate.tpr
>> The error is
>> Fatal error:
>> Invalid atom number 6518 in indexfile
>> How can i fix this ?
>> Thank so much for any help !
>> Regards,
>> KT
>> --
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================