AMBER Archive (2007)

Subject: AMBER: Reg COM restraint to DNA

From: D.Usharani (usha_at_ipc.iisc.ernet.in)
Date: Wed Jun 06 2007 - 04:56:00 CDT

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:
*********************
&rst
   iat= -1,-1, nstep1=1, nstep2=50000,
  iresid=0,irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
   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 =
12,29,62,92,125,157,189,221,253,283,316,346,391,408,441,471,504,536,568,600,632,662,695,725,0,
   grnam1='C6','P','P','P','P','P','P','P','P','P','P','P','C6','P','P','P','P','P','P','P','P','P','P','P',
   igr2 =
770,787,820,850,883,915,947,979,1011,1041,1074,1104,1149,1166,1199,1229,1262,1294,1326,1358,1390,1420,1453,1483,0,
   grnam2='C6','P','P','P','P','P','P','P','P','P','P','P','C6','P','P','P','P','P','P','P','P','P','P','P',
/
***********************
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
DNA?

Thanks in advance
usha
IIsc
bangalore

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