AMBER: Reg COM restraint to DNA

From: D.Usharani <>
Date: Wed, 6 Jun 2007 15:26:00 +0530 (IST)

Dear Amber users,

I was using a center of mass restraint for two dodecamer DNA seperated by
certain distance by defining Phosphrous. By this i found that there is
distrotion in the strucutre by loss of base pair stacking.
my input is as follows:
   iat= -1,-1, nstep1=1, nstep2=50000,
   r1=0.00000, r2=112.0000, r3=112.0000, r4=200.0000,
      rk2=5.0000, rk3=5.0000,
   r1a=0.00000, r2a=110.0000, r3a=110.0000, r4a=200.0000,
      rk2a=5.0000, rk3a=5.0000,
   igr1 =
   igr2 =
As grnam has a limit of giving 200atoms, i can't define all atoms.
with iresid=1 it says maxgrp =3 exceeded error.

So could any one guide me what way i have to define the centre of mass for

Thanks in advance

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jun 10 2007 - 06:07:09 PDT
Custom Search