AMBER Archive (2002)

Subject: Conterions

From: Monica (monicdbs_at_iitr.ernet.in)
Date: Sat Nov 16 2002 - 02:10:15 CST

Dear Sir,
I have 2 problems:

1) While doing DNA-drug minimization using NMR restraints in vacuum in
presence of conterions ,the sodium ions are forming triangulated structure
with Phosphate of DNA. First I minimize conterions but in that step only
it forms triangulated structure with Phosphate of DNA. I have tried
minimization with slow heating too (I am doing it only at 300 K)

2) Secondly I don't want to put group input on DNA while doing
minimization but removal of group input leads planer rings of DNA -drug
to be distorted.

What shall I do?
Thank you for ant help.

Monica
Deptt Biotech
IITR, Roorkee
India