[gmx-users] Atom names mismatch - PyMol retain order

[George Abadir]

Thank you very much for the hint :)
Cheers,
George

Erik Marklund wrote:

> Martin Höfling skrev:
>
>> Am Freitag, 30. Mai 2008 schrieb George Abadir:
>>
>>  
>>
>>> atoms. Then in the simulation I used the initial PDB file generated by
>>> PYMOL. Does this make things any more reasonable. Because actually, 
>>> this
>>> happened in five different simulations till now!!!! So, I don't 
>>> think it
>>>     
>>
>>
>> Just as a side comment on using PYMOL: If one wants to preserve 
>> ordering of atoms on loading and thus exporting one can set this 
>> (e.g. in the .pymolrc).
>>
>> This is what I use for editing molecules generated with pdb2gmx.
>> ...
>> set retain_order,1
>> set pdb_retain_ids,1
>> ...
>>
>> Best
>>     Martin
>>   
>
> Now that is one extremely good tip! I shall remember that.
>
> /Erik
>