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?
Thanks,
Carlos Simmerling <carlos.simmerling.gmail.com> 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 <esther_brugger.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!
Esther B.
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Received on Sun Mar 04 2007 - 06:07:26 PST
