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

Christopher Neale chris.neale at alum.utoronto.ca
Fri Apr 15 07:29:40 CEST 2016

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 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 ?

Thank you,

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