AMBER Archive (2007)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Mar 01 2007 - 06:10:55 CST

can you tell us what you did? send the sander run script and input.

On 2/28/07, Esther Brugger <esther_brugger_at_yahoo.com> wrote:
>
> 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_at_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_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!
> >
> >
> >
>
>
> Esther B.
>
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>

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