AMBER Archive (2008)

Subject: Re: AMBER: regad-tutorial-dna-polyAT

From: jani sahil (genomejani_at_gmail.com)
Date: Sun Dec 07 2008 - 23:13:30 CST

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_at_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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