[gmx-users] C36 cyclopropanated lipids in Gromacs

[Ariel Leong]

Thanks for the suggestion, I'll have a try at the converter.


On Wed, Jun 11, 2014 at 5:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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> Gromacs Users mailing list
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-- 
Best regards,
Leong Siew Wen
Institute for Research in Molecular Medicine
Universiti Sains Malaysia

“Making the simple complicated is commonplace; making the complicated
simple, awesomely simple, that’s creativity.”
 *- Charles Mingus-*