Dear AMBER Users
I am a new user of Amber and I have a query regarding adding restraints. I
am trying to run thermodynamic Integration of Protein-ligand solvated in
water box. I want to add distance restraints between protein and ligand in
order to avoid movement of ligand from its active site. I don’t want to
recompile Amber as after editing the *“map.DG-AMBER”* (as its not
recognizing DRG) I will have to…
So, I thought of manually making DISANG file (as per mailing list
recommendation for less no. of bonds).
I am not sure if, I am placing the correct values in DISANG file…... Eg.
If I want to add restraints between O (glu) and H22 (drg) and the actual
distance between them is 2.16 Amst. *“70 GLU O 261 DRG H22 2.16”*
And the second one is between H(ala) and O17(drg) and distance being 2.14.
*“72 **ALA** H 261 DRG O17 2.14“ *both with force constant of 20.
*restraints on first non-bonded pair of atoms*
*#70 GLU O 261 DRG H22 2.16*
* &rst iat= 1122, 4157, r2= 2.16, r3= 2.16,*
* r1= 0.0, r4= 20.0, rk2= 20.0, rk3= 20.0, ialtd= 0, ir6= 1,*
* /*
*#distance restraint on second pair*
*#72 **ALA** H 261 DRG OH 2.14*
* &rst iat=1143,4159, r2= 2.14, r3= 2.14,*
* / *
Can anyone please suggest if, I have used the correct values in above DISANG
file?
--
Thanks
Sunita Gupta
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Received on Thu May 13 2010 - 01:30:05 PDT
