----- Original Message -----
From: Sai Pooja <[email protected]>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: [email protected], Discussion list for GROMACS users <[email protected]>
> 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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