AMBER Archive (2006)

Subject: Re: AMBER: fixing residues

From: Prabhakar. G. (prabha.ganesan_at_gmail.com)
Date: Wed Jul 05 2006 - 22:57:38 CDT

Thanks for the help, I was able to fix the desired residues using the ibelly
option,
it works.

On 7/4/06, a a <patd_2_at_hotmail.com> wrote:
>
> Hi!
>
> You may tried to follow the descriptions in Tutorial 2 Section 5.
>
> aa
>
>
> >From: "Prabhakar. G." <prabha.ganesan_at_gmail.com>
> >Reply-To: amber_at_scripps.edu
> >To: amber_at_scripps.edu
> >Subject: AMBER: fixing residues
> >Date: Mon, 3 Jul 2006 17:46:46 +0530
> >
> >Dear Amber community,
> >
> >we are trying to do a md simulation of a particular loop of a protein,
> >The protein has a total of 398 residues and the loop regions include
> >residues 228-241.
> >is there any option in amber to fix or freeze the conformation of other
> >residues except that of loop
> >so that they do not move during the simulation.
> >
> >prabhakar
> >National Inst of Virology
> >Pune
> >India
>
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-- 
Prabhakar.G
Project Assistant,
Bioinformatics and Data Management,
National Institute of Virology,
20-A, Dr. Ambedkar Road,
Pune-411 007
Maharastra
India

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