[gmx-users] Is cholesterol model available in Charmm36 ff?

[Justin Lemkul]

On 3/19/14, 5:06 AM, davhak wrote:
> Thanks very much again for the updated charmm36 ff for Gromacs
> (http://mackerell.umaryland.edu/CHARMM_ff_params.html).
>
> Comparison of CHL1 residue records reveals only atom ordering difference for
> the atoms from 2 to 4 inclusive. In your version these atoms are ordered as
> follows:
>
>
>
> Probably this order is somewhat outdated since in the December release of
> the charmm36 the order has been changed to make the hydrogen atoms follow
> the heavy atoms i.e.:
>
>
>

I don't see anything printed above.

> This kind of atom ordering difference is probably not a problem for Gromacs,
> but probably to be compatible with charmm36 one may consider reordering of
> these atoms?
>

Sorry, without context I really don't know what the problem might be.  For any 
simulation software, the order of the atoms in the topology and the 
corresponding coordinate file need to match.  What we just released is an .rtp 
entry for CHL1, such that you can produce the topology with pdb2gmx.  The output 
coordinate file is guaranteed to match the topology.  The order of atoms in the 
input coordinates relative to the .rtp entry is irrelevant; the output topology 
and coordinates will match.

-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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