[gmx-users] Non-bonded interaction.

[Justin Lemkul]

On 5/30/14, 11:51 AM, 라지브간디 wrote:
>
> Dear justin,
>
> Thank your for your clear answer.
>
> The parameters are specifically written for CHARMM force field based on the experimental results.
>
> Particularly, charges and non-bonded interaction values for ligand molecule of CO ( Carbon Monoxide) in Myoglobin are written in literature.
>
> Since Gromos 43a1 has parameter for heme with CO, therefore I asked you " Is that possible to use only this CO ligand charges and non-bonded values derive
>
> d from experimental and written in CHARMM ff ?.
>
> In other case, shall I use this CHARMM ff values for CO in CHARMM27/36 provided by groamcs  without doing any conversion ?
>

Yes, you need to convert the units (CHARMM and Gromacs use different 
conventions), but otherwise those parameters can be used directly with CHARMM27 
or CHARMM36.

-Justin

> Thanks in advance.
>
> On 5/29/14, 10:13 PM, ????? wrote:
>> Dear Justin,
>>
>> Thanks for your
>> reply.
>>
>> I am not mixing up the parameter here.
>> What i am trying to do here
>> In order to reproduce the dipole moments of the CO, I have to
>> follow up the specific charges and non-bonded interaction values specified in
>> literature in CHARMM format ( For C atom, charge -0.75, ?=0.0262
>> & ? = 3.83) ( For O atom, charge -0.85, ?=0.0262 & ? =
>> 3.83).
>
> "CHARMM format" and "CHARMM force field" are different, so what is the origin of
> those parameters? Were they developed specifically for CHARMM or some other
> force field? If these parameters were not specifically designed to be
> consistent within Gromos96 43A1, my original point stands - they cannot be
> combined with a force field for which they were not self-consistently derived.
>
>> Could you tell how it can be done? If i cant use them in
>> gromos43a1 ff, possible to use in charmm27 provided by gromacs package? or it
>> does need any conversion to use in gromacs-charmm27 ff?
>>
>
> Both CHARMM27 and CHARMM36 are fully supported by 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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