AMBER Archive (2009)

Subject: Re: [AMBER] solvent accessible surface area

From: Ray Luo (ray.luo_at_uci.edu)
Date: Thu Oct 08 2009 - 13:17:09 CDT

Dear Siddharth,

You can find atom-based SASA data in the pbsa output file when setting
npbverb=1.

Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

Siddharth Rastogi wrote:
> Hello Amber users,
> I am interested to get SASA for hydrophobic groups and hydrophilic groups in
> protein separately. How to get these values?.
>
>
> On 9/23/09, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
>
>> i suggest using imin=5, using the -y flag to read the trajectory (see the
>> manual for details).
>> set igb>0 (exact value doesn't matter if you aren't interested in solv
>> energy), gbsa=2 and surften=1, and the Esurf will be the SASA.
>>
>> On Wed, Sep 23, 2009 at 3:26 PM, Ganesh Kamath <gkamath9173_at_gmail.com
>>
>>> wrote:
>>>
>>> For a trajectory. The file is a mdcrd file format of AMBER. I could also
>>> convert the mdcrd file
>>> to a bunch of PDBs.
>>>
>>> thanks,
>>> ganesh
>>>
>>> On Wed, Sep 23, 2009 at 3:20 PM, Carlos Simmerling <
>>> carlos.simmerling_at_gmail.com> wrote:
>>>
>>>
>>>> for a snapshot, or a full trajectory? what format are the coordinates?
>>>>
>>>> On Wed, Sep 23, 2009 at 3:07 PM, Ganesh Kamath <gkamath9173_at_gmail.com
>>>>
>>>>> wrote:
>>>>>
>>>>> Hi Amber Users,
>>>>>
>>>>> Could anyone tell me how to calculate the solvent accessible surface
>>>>>
>>>> areas
>>>>
>>>>> for a protein in explicit water.
>>>>>
>>>>> thanks,
>>>>>
>>>>> ganesh
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>
>
>
>
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