[gmx-users] GROMACS compatible Charmm36 Phospho residues

[Justin Lemkul]

On 10/23/15 2:45 PM, Parker de Waal wrote:
> Thanks Jason for the quick reply,
>
> However I'm a bit concerned about the residue geometry (http://i59.tinypic.com/tar8m9.png), It looks as if the O3P atom is too far from the phosphate group.
>
> Is this normal for SP2 residues in CHARMM?
>

That's definitely wrong, as if there isn't even a bond between those atoms.  But 
I don't see how that would be possible, as the .rtp file correctly defines the 
bonds.  That atom is OT, not O3P (we have O1P, O2P, and OT in the SP2 residue) - 
did you change the .rtp file?  If you changed the name, you probably didn't 
change it in the [ bonds ] directive as well, and hence you would be missing a 
bond in the topology.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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