[gmx-users] Topology for Sphingomyelin

[Ganesh Shahane]

Thank you for your reply Justin!. It was helpful.

On Fri, Jan 22, 2016 at 2:41 PM, Justin Lemkul <jalemkul at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Best Regards,
Ganesh Shahane