[gmx-users] Topology for Sphingomyelin

[Ganesh Shahane]

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?

On Fri, Jan 22, 2016 at 4:29 PM, Ganesh Shahane <ganesh7shahane at gmail.com>
wrote:

> 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
>



-- 
Best Regards,
Ganesh Shahane