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
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Received on Fri May 20 2011 - 07:30:03 PDT
