AMBER Archive (2008)

Subject: Re: AMBER: about SASA and AMBER

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Oct 20 2008 - 12:17:42 CDT

another option is to read in your trajectory using sander with imin=5
(amber9 or 10, make sure it is fully patched).
then, set surften=1 and your Esurf will be the sasa. sander will read
each frame and write the info.
carlos

On Mon, Oct 20, 2008 at 1:07 PM, Lachele Foley (Lists)
<lf.list_at_gmail.com> wrote:
> We use ptraj and then naccess and a homemade program to do that.
>
> naccess: http://www.bioinf.manchester.ac.uk/naccess/
>
> Write off-list if you're interested in the program.
>
>
>
> On Mon, Oct 20, 2008 at 11:58 AM, Yunierkis Perez Castillo
> <Yunierkis_at_uclv.edu.cu> wrote:
>> Hi all
>> Is there any way I can keep track of the changes in the SASA of a protein or certain region of a protein along a MD trajectory??
>> I have looked in the ptraj manual but there is no command to performs such calculation.
>> Thanks in advance for any help.
>> Yunierkis
>>
>> Servicio de Correos de la Universidad Central "Marta Abreu" de Las Villas. http://www.uclv.edu.cu
>> -VI Conferencia Internacional de Ciencias Empresariales, del 16 al 18 de octubre de 2008, Cayo Santa Mar?a, Cuba. http://economia-publica.uab.es/VIcubaCICE.doc
>> -V Conferencia Cient?fica Internacional de Ingenier?a Mec?nica, COMEC 2008, del 4 al 6 de noviembre de 2008, UCLV, Cuba. http://eventos.fim.uclv.edu.cu/comec
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>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
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