AMBER: regad-tutorial-dna-polyAT

From: balaji nagarajan <>
Date: Mon, 8 Dec 2008 10:15:10 +0530

Dear Amber .,
I have tried the tutorial about the polyAt dna dynamics
for explicit solvent .,
I haave no problem in generating nuc_ter.pdb and solvating
it in solvateoct and viewed the structures in xleap it depicts the same as the tutorial
I can also able to do it for the minimization run
for the both scripts namely &

when I viewed the structures through vmd its the same as that in tutorial ..,

but I faced a problem while running the script

when I viewed th eoutput file(*.mdcrd)
in vmd after loading the *.prmtop file
the bondings all are different and the dynamics is not as
wat it mentioned

I dont know the problem
help me out to solve

I have attached the files ....

thanks in advance

Search for videos of Bollywood, Hollywood, Mollywood and every other wood, only on

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)

Received on Mon Dec 08 2008 - 01:14:31 PST
Custom Search