AMBER Archive (2008)

Subject: AMBER: regad-tutorial-dna-polyAT

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Sun Dec 07 2008 - 22:45:10 CST

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
polyAT_wat_min1.in & polyAT_wat_min2.in

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

but I faced a problem while running the script
polyAT_wat_md1.in

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

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