AMBER Archive (2007)

Subject: Re: AMBER: solvent accessible surface area (SASA)

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Feb 28 2007 - 16:50:20 CST

you might try using the gbsa optino, especially gbsa=2 and surften=1. this
way the SASA energy will actually be the SASA. You can use imin=5 to read
the
trajectory and report SASA for each frame.

On 2/28/07, Esther Brugger <esther_brugger_at_yahoo.com> wrote:
>
> Dear Everyone,
>
> I am trying to calculate the "solvent accessible surface area (SASA)" of a
> molecule through a trajectory file obtained by MD simulation (AMBER8). I
> removed the water molecules (TIP3P model) and counter ions from the systym
> by using Ptraj. I have some problems to do the calculation of SASA.
>
> (1) I checked the archive file for the discussion, it seems "molsurf"
> program can calculate SASA if I put the proble radius at zero, is it
> correct? But it need pqrfile, I really don't know how I can get this file.
> And is it possible to calculate SASA by mdcrd trajectory file in molsurf?
> (2) Someone suggested to use the software (SURFace) in Honig Lab, but I
> found it needs the pdb file for the calculations. Is there someone know how
> to convert the trajactory (mdcrd) file to pdb file for each of the frame?
> (3) I also found somebody suggested to usd the software "naccess", but I
> met some problems to decrypt the file, because I didn't find the commands
> "crypt/des/mcrypt" in my Linux system. Dose someone could give me some
> suggestions about that?
>
> Sorry, I post a lot of questions, I really wish someone could help me to
> solve these problelms,
> Thanks for your any help!
>
>
>

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