use ptraj to remove the water with the strip command. you can't calculate
SASA with water there.
also the -c is not right for the mdcrd file. check the amber manual for
details.
On 3/1/07, Esther Brugger <esther_brugger.yahoo.com> wrote:
>
> Thanks for your reply. Here is the command and input file that I used.
> Acturally, this mdcrd trajactory file has the water in it, I want to
> remove the water to calculate the SASA, but I really don't know how to do
> it. Thanks again for your help!
> $AMBERHOME/exe/sander -O -i SASA.in -p prmtop -c mdcrd -o SASA.out
> &cntrl
> imin = 5,
> gbsa=2,
> surften=1
> /
>
>
>
> *Carlos Simmerling <carlos.simmerling.gmail.com>* wrote:
>
> can you tell us what you did? send the sander run script and input.
>
> On 2/28/07, Esther Brugger <esther_brugger.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.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.
> > ------------------------------
> > Bored stiff? <http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com>Loosen up...
> > Download and play hundreds of games for free<http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com>on Yahoo! Games.
>
>
>
>
>
>
> *Carlos Simmerling <carlos.simmerling.gmail.com>* wrote:
>
> can you tell us what you did? send the sander run script and input.
>
> On 2/28/07, Esther Brugger <esther_brugger.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.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.
> > ------------------------------
> > Bored stiff? <http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com>Loosen up...
> > Download and play hundreds of games for free<http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com>on Yahoo! Games.
> >
>
>
>
>
>
> Esther B.
>
> ------------------------------
> Finding fabulous fares is fun.
> Let Yahoo! FareChase search your favorite travel sites<http://farechase.yahoo.com/promo-generic-14795097;_ylc=X3oDMTFtNW45amVpBF9TAzk3NDA3NTg5BF9zAzI3MTk0ODEEcG9zAzEEc2VjA21haWx0YWdsaW5lBHNsawNxMS0wNw--%0A>to find flight and hotel bargains.
>
>
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Received on Sun Mar 04 2007 - 06:07:39 PST
