[gmx-users] simulation of heme along with h2o2

[Justin Lemkul]

On 2/19/15 6:44 AM, Sanchaita Rajkhowa wrote:
> 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.
>

In principle, modification of the .hdb is all that you need to do.  Did your 
additions not fix anything?  Or do you just have errors (hopefully fewer) that 
persist?  The alternative is to upload the structure to the CHARMM-GUI server. 
It will process the whole thing and write a coordinate file that is fully 
compliant with the CHARMM force field (and provide GROMACS inputs for you).

-Justin

> 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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>>
>>

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

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

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