[gmx-users] Updated CHARMM36 force field files available

Guillaume Chevrot guillaume.chevrot at gmail.com
Mon Nov 17 22:22:22 CET 2014

Le 17/11/2014 18:32, Justin Lemkul a écrit :
> On 11/17/14 6:04 AM, Guillaume Chevrot wrote:
>> Dear Justin,
>> thanks for the new version of the charmm36 force field.
>> I have a question concerning the file merged.hdb.
>> I noticed that ADP has disappeared from this file. As consequence, 
>> pdb2gmx now
>> (it was not the case with previous release charmm36-mar2014) complains:
>> WARNING: atom H4' is missing in residue ADP ....
>> Is there a good reason to have made this modification?
> It wasn't removed; our released force fields have never had ADP in the 
> .hdb file.  The .hdb is written manually, so it doesn't cover 
> everything in the .rtp file.
OK. So maybe it could also be added in the next release by default? If I 
can help ...

>> I also noticed that there is no entry in merged.hdb for TP2 (the 
>> dianionic
>> phosphotyrosine).
> I will add these for the next release.  For the dianionic species, the 
> .hdb will be the same as the unphosphorylated residue, minus the 
> hydroxyl H.  The monoanionic are the same, with hydroxyl syntax for 
> the HPO4 atom the same as any other hydroxyl.  Let me know if you need 
> help adding these.
Thanks, I had already added the entry I needed. I was just a bit 
surprised it was not already there.


> -Justin

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