[gmx-users] simulation of heme along with h2o2

[Sanchaita Rajkhowa]

Hi, I tried using charmm forcefield to simulate heme but we are getting
warning messages.

WARNING: atom HA is missing in residue HEME 1500 in the pdb file
.
.
.

for all 30 hydrogens.

Later we tried modifying the aminoacids.hdb as:

HEME    3
1       5       HA      CA      N       C       CB
1       1       HE1     CE1     CD1     CZ
1       1       HE2     CE2     CD2     CZ

But the problem still persists. What should be done?? Please help.

regards,
Sanchaita.


On 19 February 2015 at 09:43, Sanchaita Rajkhowa <srajkhowa18 at gmail.com>
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.
>
> 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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>