[gmx-users] Capping residues

[Mark Abraham]

----- Original Message -----
From: Sai Pooja <saipooja at gmail.com>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-users at gromacs.org>

> I am sorry if I did not frame the question correctly, but putting it very simply, is there a way to use capping residues with the charmm forcefield if the residues are --COCH3 and NHCH3?

Yes - you edit a copy of the .rtp file in your working directory and add whatever you want. Here's what I use in CHARMM

[ ACE ]
 [ atoms ]
        CH3     CT3     -0.270  0
        HH31    HA      0.090   0
        HH32    HA      0.090   0
        HH33    HA      0.090   0
        C       C       0.510   1
        O       O       -0.510  1
 [ bonds ]
        C       CH3
        C       +N
        CH3     HH31
        CH3     HH32
        CH3     HH33
        O       C
 [ impropers ]
        C       CH3     +N      O

[ NAC ]
 [ atoms ]
       N       NH1     -0.470  1
       HN      H       0.310   1
       CH3     CT3     -0.110  1
       HH31    HA      0.090   1
       HH32    HA      0.090   1
       HH33    HA      0.090   1
 [ bonds ]
       -C      N
       N       HN
       N       CH3
       CH3     HH31
       CH3     HH32
       CH3     HH33

 [ impropers ]
       N       -C      CH3     HN
       -C      CH3     N       -O

Mark

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