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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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