Re: [AMBER] Restrained MD with COM restraint with PMEMD

From: case <>
Date: Tue, 3 Dec 2013 21:33:17 -0500

On Tue, Dec 03, 2013, Mike Limb wrote:
> In each of these MD simulations I fix the ligand in position using a COM
> restraint that is specified in rc.con
> # COM restraint with NAM-D and CD of Glu35 (between 1 and 6 A)
> &rst
> r1=-500,r2=1.0,r3=6.0,r4=500,
> rk2=50,rk3=50,
> iresid=1,
> iat=130,35,
> ATNAM(1)='C1','C2','C3','C4','C5','O5',
> ATNAM(2)='CD',
> /

Try using the simpler form for COM restraints, in which you have iresid=0,
and use iat<0 to indicate a com group and igr1 to give the atom numbers in the

[Are you sure the above works in sander? You syntax looks wrong: atnam(1) is
supposed to be a four-character string, and you are giving it something very


AMBER mailing list
Received on Tue Dec 03 2013 - 19:00:03 PST
Custom Search