[gmx-users] Atom names mismatch

[George Abadir]

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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