[gmx-users] CHARMM36 force field available for GROMACS

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Dear Justin,

Did you provide/add the parameters for Zn bound to OH- (hydroxide ion) and Zn bound to H2O (water) in updated CHARMM36 ff? For example, this state is important for some structures. E.g. Carbonic anhydrase.

Ahmet Yıldırım


18 Mar 2014 tarihinde 18:44 saatinde, Justin Lemkul <jalemkul at vt.edu> şunları yazdı:

> 
> Hi All,
> 
> To follow up on a few recent issues that we have discovered and/or have been reported here, we have updated our CHARMM36 force field files.  As always, they can be downloaded from:
> 
> http://mackerell.umaryland.edu/CHARMM_ff_params.html
> 
> Here is a list of changes:
> 
> 1. An error in ions.itp was propagated from the old CHARMM27 files, which assigned a -2 charge to Zn.  The .rtp entry for Zn was correct, so if you are studying any metal-containing proteins, the simulations should be fine if the topology was generated with pdb2gmx.  It would only matter if you used genion to add Zn to the system, so the error would be fairly obvious in the accumulation of negative charge.
> 
> 2. An atom name in the LSN (neutral lysine) .rtp entry was incorrect.  This is also a rather obvious error, as pdb2gmx would die with a fatal error when trying to generate impropers.
> 
> 3. Per recent posts to the list, we have corrected errors related to H5' nomenclature in RNA.  Bonds would have been missing between C5' and H5'1/H5'2, causing H atoms to go flying around, or the simulation may have just simply crashed.  DNA simulations done with this force field are not affected by this problem.  Support for RNA has further been enhanced by the addition of .hdb entries for ADE, CYT, GUA, and URA.
> 
> 4. We have added angle parameters for NH2-CT1-CT1 to fix a problem with missing angle parameters for neutral N-terminal amino acids like Ile and Thr.
> 
> 5. We added heme and cholesterol (CHL1), per user requests.
> 
> If anyone has comments, questions, etc. about these force field files, please feel free to post them here or send them to me.
> 
> Happy simulating!
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
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