[gmx-users] what is the source of "CHL1" cholesterol in the gromacs charmm port?

[Christopher Neale]

Thank you very much Justin!

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: 15 April 2016 05:46
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] what is the source of "CHL1" cholesterol in the gromacs charmm port?

On 4/15/16 1:29 AM, Christopher Neale wrote:
>
> Dear Users:
>
> When I look at charmm36-jun2015.ff/merged.rtp downloaded from
> http://mackerell.umaryland.edu/charmm_ff.shtml , it has a cholesterol
> molecule named CHL1. However, I do not find such a molecule in the
> charmm-specific toppar_c36_feb16.tgz downloaded from the same site. In the

Just a note to everyone: as the dates should make very obvious, the Feb 2016
release of the CHARMM force field is much newer than the port; you should not
expect exact agreement between these files.  I have not yet made an updated
port, but it's on my to-do list.

> later tarball, I do find cholestrol as "RESI CLOL" in top_all36_cgenff.rtf
> but that is from cgenff and the values differ. As a simple proof of the
> difference, the charge on O3 is not the same, though the differences extend
> beyond that.
>
> Some comments in the charmm-format files refer to
> toppar_all27_lipid_cholesterol.str , but I can not find that file ... I
> checked in toppar_c31b1.tar.gz from the same website but to no avail.
>
> So my question is what is the source for CHL1 in
> charmm36-jun2015.ff/merged.rtp ?
>

toppar/stream/lipid/toppar_all36_lipid_cholesterol.str

Many residues come from the stream files (either from residues found there or
created from patches therein).

-Justin

--
==================================================

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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