[gmx-users] Updated CHARMM36 force field files available

[Guillaume Chevrot]

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?


I also noticed that there is no entry in merged.hdb for TP2 (the 
dianionic phosphotyrosine).


Best,

Guillaume



On 11/06/2014 01:57 AM, Justin Lemkul wrote:
>
> All,
>
> I upload a new version of the GROMACS port for the CHARMM36 force 
> field today. You can find the files at:
>
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>
> We have steadily been adding to these files since the last release in 
> March. Most fixes are trivial nomenclature adjustments and changes 
> related to a few bugs that were propagated in files found in 
> charmm27.ff that were subsequently fixed.  All were things that would 
> have been obvious because they would have triggered fatal errors when 
> running pdb2gmx.
>
> New in this version of the force field are:
>
> 1. Changed nucleic acid nomenclature (H5' and H5'') for ease of 
> interfacing with CHARMM-GUI
> 2. New atom type for Mg2+ to use parameters from 
> dx.doi.org/10.1021/ct3000734, see MG entry in ions.itp for the 
> "define" keyword
> 3. Addition of phosphorylated amino acids (mono- and dianionic forms 
> of Ser, Thr, and Tyr)
> 4. Addition of bacterial lipids
> 5. Addition of S-adenosyl methionine
>
> Happy simulating!
>
> -Justin
>