[gmx-users] Going from OPLS-AA dihedrals to CHARMM22 dihedrals.

[Dawid das]

That's what I thought. Thank you for your help.

Best regards,
Dawid


2014-07-16 12:53 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 7/16/14, 6:51 AM, Dawid das wrote:
>
>> Dear Justin,
>>
>> In this case may I use Ryckaert-Bellemans dihedral (func. type 3) for one
>> part of the new residue and proper dihedral (multiple) (func. type 9) for
>> the rest? Is this "mixing" allowed?
>>
>>
> No.  Force fields are self-consistent entities; even what may seem like a
> minor change can have major implications.  CHARMM uses periodic dihedrals,
> so hacking in some R-B dihedrals that exist in another force field makes no
> sense at all.
>
> -Justin
>
>
>
>> 2014-07-16 1:34 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>>>
>>> On 7/15/14, 1:29 PM, Dawid das wrote:
>>>
>>>  Dear Gromacs experts,
>>>>
>>>> I have following issue. I need torsional parameters from this
>>>> publication:
>>>> D. V. Dmitrienko et al., Biochemistry (Moscow), 2006, Vol. 71, No. 10,
>>>> 1133-1152
>>>> where OPLS-AA FF has been used but I need to adapt them for CHARMM22 FF.
>>>> Now the thing is that there are two different torsional energy
>>>> expression
>>>> used in those FFs.
>>>> How can I go from one to another?
>>>> To be precise I want to adapt parameters from the above mentioned
>>>> publication to expression  for torsional potential from this
>>>> publication:
>>>>
>>>> N. Reuter et al., J. Phys. Chem. B, 2002, Vol. 106,  6310-6321
>>>>
>>>> Any help will be appreciated.
>>>>
>>>>
>>>>  It's not wise to try to hack parameters developed for one force field
>>> into
>>> another.  Dihedrals are especially dangerous, because their validity is
>>> also dependent upon the nonbonded interactions of atoms 1 and 4 in the
>>> interaction; differences in charges and LJ parameters between OPLS-AA and
>>> CHARMM will make the dihedral non-transferable.
>>>
>>> -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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