[gmx-users] simulation of heme along with h2o2

[Justin Lemkul]

On 2/18/15 11:13 PM, Sanchaita Rajkhowa wrote:
> Dear Justin, thank you for the reply. However, I would like to know if
> there is any server which can generate parameters for heme to be used in
> OPLS-aa? We have already tried in swissparam with failed results. Please
> help.
>

I have no idea if OPLS-AA even supports heme, or if there is any server that 
writes OPLS-AA topologies.  There is no need for SwissParam; our force field 
files for CHARMM36 have supported heme for a long time:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

-Justin

> On 18 February 2015 at 21:15, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/18/15 9:18 AM, Sanchaita Rajkhowa wrote:
>>
>>> Dear all, I am trying to simulate a heme containing protein in high
>>> concentration (having hydrogen peroxide). However, I do not know which
>>> forcefield to use. Heme has forcefield in gromos96 but not the forcefield
>>> of H2O2? Will generating .itp files for H2O2 from swissparam work? Please
>>> help.
>>>
>>>
>> SwissParam creates CHARMM-compatible parameters, so no, you can't mix
>> those with GROMOS.  CHARMM supports heme, but you have to clean up a lot of
>> auto-generated angles and dihedrals that don't belong.
>>
>> -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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-- 
==================================================

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

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