Dear Amber Users
I need help with a basic restrained A-DNA simulation in water. I generated
an A-DNA with a particular sequence using the 'nab' program. To minimize
the DNA, I used torsional restraints for some of the sugar and backbone
dihedrals and carried out a minimization in water. However, the minimized
structure was no longer an A-DNA and the final restraints printed in the
mdout file show severe penalties and great deviations from the desired
angles.
To check what the problem is, I went a step back and visualized the leap
generated pdb and it was a perfect A-DNA. However, when I loaded the leap
generated crd file on the leap generated topology file, the structure
looked severely distorted. And since this crdfile is the starting structure
for my minimization, I guess the A-DNA structure was disturbed during
minimization.
For re-confirming, I visulalized the leap generated crd and topology files
given in the Amber tutorials Section B1 (Simulation of DNA) and even that
structure was distorted. Where am I going wrong? And how do I restraint the
A-DNA to its conformation?
Thanks in advance for your suggestions
--
Debostuti
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 05 2014 - 02:30:03 PST
