Re: AMBER: solvent accessible surface area (SASA)

From: Esther Brugger <>
Date: Wed, 28 Feb 2007 15:54:51 -0800 (PST)

Dear Carlos,
 Thanks a lot for your reply.
 I tried as you said, it has some prolems when it runs. it shows:
 forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
 Image PC Routine Line Source
 sander 081A86F6 Unknown Unknown Unknown
 I don't know why......Do you have any suggestion for that?

Carlos Simmerling <> wrote: 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 <> 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!


Esther B.

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Received on Sun Mar 04 2007 - 06:07:26 PST
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