[gmx-users] Atom names mismatch

[George Abadir]

I am aslo using the ffamber port to GROMACS is this helps.
Thank you very much,
Regards,
George

George Abadir wrote:

> Thanks for your reply. I built the molecule using PYMOL, then used 
> pdb2gmx to generate the topology. It seems that pdb2gmx reorders the 
> 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 is a mere coincidence. The molecule at the end is intact and 
> all the atoms are in their respective positions (i.e., the carbon was 
> not actually exchanged with hydrogen as it should be from the 
> warning). It would very helpful if someone could see how these 
> simulations continued without deforming the molecule.
> Thank you very much,
> Regards,
> George
>
> Mark Abraham wrote:
>
>> George Abadir wrote:
>>
>>> Thank you very much for your reply. Actually I ran the whole 
>>> simulations (1000000 time steps), and the system did not crash. The 
>>> molecule still 
>>
>>
>>
>> I'm extremely surprised. Perhaps bond constrains on all atoms were 
>> your friends here. :-) Nonetheless, it seems likely from the 
>> mismatches that some incorrect van der Waals models were applied.
>>
>>> has the structure of phenylalanine. Does this mean that the final 
>>> coordinates are ok, or should I redo the simulation again after 
>>> resorting the atoms.
>>
>>
>>
>> Without understanding the reason for the mismatch, you can't say the 
>> simulation is OK with certainty. It looks like the phenylalanine 
>> structure you generated for the simulation ordered its atoms 
>> differently from the one you used to generate its topology. If you go 
>> and re-order the atoms in the structure file according to the 
>> topology file, you should see these warnings go away, and now you can 
>> be confident a resulting simulation is OK. I wouldn't trust the first 
>> one, though.
>>
>> Mark
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