Dear Ganesh,
You can also use the ATB site, and convert the all atom .itp to CHARM36 format, or build it (charge, bond, angles, etc...) from the already present CHARMM36 atom parameters. Check your charges if you get them from the ATB.
Stephan Watkins
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
http://mackerell.umaryland.edu/~jalemkul
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> 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
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
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Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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