[gmx-users] cholesteryl oleate parameters-reg

Justin Lemkul jalemkul at vt.edu
Wed Jun 19 17:33:49 CEST 2013

On 6/19/13 9:46 AM, Revthi Sanker wrote:
> ​Dear all,
>   I found a paper where they have updated
> the c36 forcefield to include cholesterol parameters ( to which I should be able to modify by adding an oleate chain to get my cholesteryl oleate
> moiety) :
> http://pubs.acs.org/doi/pdf/10.1021/jp207925m
> and I found this link:
> http://lists.gromacs.org/pipermail/gmx-users/2010-October/054515.html  and further obtained the file:  toppar_all36_lipid_cholesterol.str
> file. Should I try converting *.str file to an itp file that is compatible with
> gromacs or can I add this as a new molecule to the existing lipids.rtp
> in the charmm36.ff folder? Which would be a cleaner way of doing it? I
> am unable to decide in this regard. Kindly provide me your valuable
> suggestions.

It doesn't really matter which way you go.  The "cleaner" way depends on what 
type of coordinate file you have already.  If you have a pre-built configuration 
with molecules whose atoms conform to the force field expectations (atom names 
and presence of hydrogens), I'd say just make an .itp file.  If you need to 
construct hydrogen positions, build .rtp and .hdb files.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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