On 1/22/16 7:43 PM, Ganesh Shahane wrote:
Hi Justin,
I have stumbled upon another problem. The sphingomyelin topology (PSM.itp)
that Charmm-GUI provides has an atomtype called NHL that is not defined by
the Charmm36 ff. I am using the latest charmm36-jun2015.ff. Could you
please look in to this?
As I said, the charmm36.ff distribution we provide is not going to work because
parameters related to sphingolipids will not be there. But CHARMM-GUI gives you
an all-inclusive force field file that has everything you need.
-Justin
On Fri, Jan 22, 2016 at 4:29 PM, Ganesh Shahane <ganesh7shah...@gmail.com>
wrote:
Thank you for your reply Justin!. It was helpful.
On Fri, Jan 22, 2016 at 2:41 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/22/16 8:51 AM, Ganesh Shahane wrote:
Dear Gromacs users,
I wish to simulate a mixed lipid bilayer of which one of the lipids is
sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using
Charmm36
ff. Towards this, I constructed the bilayer using Charmm-GUI but then was
surprised to find that its topology is not present in residue topology
database of Charmm36 ff.
Does anyone has any idea about where can I get topology for PSM? Or would
it be wise to submit it to paramchem to get its topology?
Use the force field CHARMM-GUI provides you. It supports everything in
your system. Our charmm36.ff port may not include everything; I extend it
only when people ask for specific parameters (as CHARMM is a huge force
field, sometimes things get missed and I rely on this kind of feedback).
I'll add sphingomyelin in the next release.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Best Regards,
Ganesh Shahane
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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