[gmx-users] problem in parametrization of NH2 group

[Justin Lemkul]

On 7/17/15 2:31 AM, Nidhi Batra wrote:
> Dear All
> I want to run a simulation for a protein-peptide complex where the N- &
> C-terminal of the peptide is capped by acetyl and amine (NH2) group
> respectively. I am using the charmm36ff but couldn't find the parameters
> for NH2 group anywhere. I tried using SwissParam to generate the .itp but
> don't know how to convert it to .rtp.
>
> Kindly help regarding this.
>

 From the CHARMM top_all36_prot.rtf:

PRES CT2          0.00 ! amidated C-terminus
GROUP                  ! use in generate statement
ATOM C    CC      0.55 !
ATOM O    O      -0.55 !     |
GROUP                  !   O=C
ATOM NT   NH2    -0.62 !     |
ATOM HT1  H       0.32 !     NT
ATOM HT2  H       0.30 !    / \
BOND C NT              !  HT1 HT2 (HT1 is cis to O)
BOND NT HT1 NT HT2     !
IMPR C NT CA O C CA NT O
IMPR NT C HT1 HT2 NT C HT2 HT1

-Justin

-- 
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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

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