[gmx-users] C36 cyclopropanated lipids in Gromacs

[Justin Lemkul]

On 6/11/14, 5:45 AM, Ariel Leong wrote:
> Thank you, Justin. I've checked that out as well, but it was also missing
> the bacterial lipids containing cyclic moieties.
>

Those can easily be added using our stream file converter on the same page. 
I'll look into adding them as standard in a future release.

-Justin

>
> On Wed, Jun 11, 2014 at 5:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/11/14, 5:14 AM, Ariel Leong wrote:
>>
>>> Hi,
>>>
>>> I'm interested to simulate lipids with cyclopropanated chains with
>>> Gromacs.
>>> The C36 parameters for the lipids have been publicly provided by Klauda et
>>> al. in CHARMM str format. I've looked at the C36 force field for Gromacs
>>> and it seems that they were not included in the package.
>>>
>>> I was wondering of charmm2gromacs-pvm.py might do the trick converting the
>>> parameter into Gromacs compatible formats or if there are other more
>>> suitable methods of doing it?
>>>
>>>
>> We provide regularly updated CHARMM36 files for Gromacs here:
>>
>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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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>
>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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