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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Received on Sun Jun 10 2007 - 06:07:09 PDT
