[gmx-users] Topology for Sphingomyelin

[Justin Lemkul]

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 <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
>>
>
>
>

-- 
==================================================

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

==================================================