Hello,
On Mon, Feb 15, 2010 at 9:30 AM, Arvind Marathe <bahuroopi.gmail.com> wrote:
> Hello,
>
> I am trying to calculate the binding energy of a receptor and a ligand
> using the MMPBSA.py module. Here is my input mmpbsa.in file:
>
>
> ---------------------------------
> Input file for running PB and GB in serial
> &general
> receptor_mask=':1-468:509-510', ligand_mask=':469-508',
> endframe=20, verbose=2,
> /
> &gb
> igb=2, saltcon=0.100
> /
> ---------------------------------
>
>
> And this is the command i used:
>
>
> ---------------------------------
> MMPBSA.py -i mmpbsa.in -sp complex_solvated.prmtop -cp complex.prmtop
> -rp receptor.prmtop -lp ligand.prmtop -y test.mdcrd
> ---------------------------------
>
>
> Here is the output i get:
>
>
> ---------------------------------
> Warning: Input error! "keep_files=2" is an invalid option.
> ptraj found! Using /data/apps/amber9_mvapich2//exe/ptraj
> 1568,1579c1331,1337
> sander found! Using /data/apps/amber9_mvapich2//exe/sander (serial only!)
> Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
> modified Bondi radii (mbondi)
>
> Preparing trajectories with ptraj...
> 20 frames were read in and processed by ptraj for use in calculation.
>
> Starting sander calls
>
> Starting gb calculation...
>
>
> mdfil: Error unknown flag: -y
The problem you have to fix is getting sander to recognize the -y
flag. All of the calculations are done using this flag (inptraj), so
that all frames are analyzed from a single trajectory file rather than
having separate inpcrds for each file.
I'm pretty sure this was a bug in a pre-patched amber9. Make sure
that all of the patches are applied, then you must recompile. Don't
forget to do "make clean" before you do "make serial" again.
Sander must be fixed before MMPBSA.py will work.
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Feb 15 2010 - 07:00:03 PST
