Dear jani .,
it worked
thank you !
Date: Mon, 8 Dec 2008 10:43:30 +0530
From: genomejani.gmail.com
To: amber.scripps.edu
Subject: Re: AMBER: regad-tutorial-dna-polyAT
Hi
load first prmtop file and then .mdcrd file and in selection column
select amber coordinates with periodic box .
Hope this might help
Regards
Jani
CDAC INDIA
On Mon, Dec 8, 2008 at 10:15 AM, balaji nagarajan <balaji_sethu.hotmail.com> wrote:
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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Received on Mon Dec 08 2008 - 01:15:41 PST
