Thank you. It is running now.
________________________________
From: Bill Miller III <brmilleriii.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Fri, May 20, 2011 10:46:37 AM
Subject: Re: [AMBER] How to use mmpbsa.py for three-trajectory protocol?
That is correct. That way the same number of frames are analyzed for all
trajectories.
-Bill
On Fri, May 20, 2011 at 10:44 AM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> I see. So if I use the input file like this:
> Input file for running PB and GB
> &general
> endframe=50, verbose=1,
> /
> &gb
> igb=2, saltcon=0.300
> /
> &pb
> istrng=0.300,
> /
>
> The endframe will be the same for complex, ligand, and receptor. It that
> right?
>
>
>
>
>
> ________________________________
> From: Bill Miller III <brmilleriii.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Fri, May 20, 2011 10:07:02 AM
> Subject: Re: [AMBER] How to use mmpbsa.py for three-trajectory protocol?
>
> You simply need to tell MMPBSA.py of the extra trajectories and prmtops for
> the receptor and ligand on the command line. You can see how to use them
> just through the usage statement:
>
> Usage: MMPBSA.py {-O} -i inputfile \
> -o output_file \
> -sp solvated_prmtop \
> -cp complex_prmtop \
> -rp receptor_prmtop \
> -lp ligand_prmtop \
> -y mdcrd1 mdcrd2 mdcrd3 ... mdcrdN \
> {-do decomp_output_file} \
> {-yr receptor_mdcrd1 ... receptor_mdcrdN} \
> {-yl ligand_mdcrd1 ... ligand_mdcrdN} \
> {-mc mutant_complex_prmtop} \
> {-mr mutant_receptor_prmtop} \
> {-ml mutant_ligand_prmtop} \
> {-srp solvated_receptor_prmtop} \
> {-slp solvated_ligand_prmtop} \
> {-xvvfile xvvfile} \
> {-make-mdins} || {-use-mdins} || {-rewrite-output}
>
> The -yr flag is for the receptor trajectory, the -yl flag is for the ligand
> trajectory, and the -srp and -slp flags are for the solvated receptor and
> ligand prmtop, respectively, if the simulations are solvated. All the other
> information (start frame, end frame, interval, etc) are placed in the
> MMPBSA.py input file and are the same for the complex trajetory.
>
> I hope that helps.
>
> -Bill
>
> On Fri, May 20, 2011 at 10:00 AM, bin wang <wang_p_z.yahoo.com.cn> wrote:
>
> > Hello everybody,
> > I am using mmpbsa.py for the calculation of binding energy. Now I want
> to
> > try
> > three-trajectory method but I cannot find how to use it in the mmpbsa.py
> > manual. Could anybody give me some suggestions? Thank you very much.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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Received on Fri May 20 2011 - 08:30:02 PDT
