That's it !
Thanks Jason
--- 10年1月15日，周五, Jason Swails <jason.swails.gmail.com> 写道：
发件人: Jason Swails <jason.swails.gmail.com>
主题: Re: [AMBER] problem with MMPBSA.py
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2010年1月15日,周五,下午4:42
On Fri, Jan 15, 2010 at 3:19 AM, xueqin pang <pangxueqintea.yahoo.com.cn> wrote:
> Jason,
>
> I get it! It works well.
>
> But there is another problem. Since the receptor of my system has two part, when I add the other part into the mmpbsa.in, it went wrong. (It works well with mmpbsa.pl)
>
> Do you have any suggestions on this problem.
>
> Thanks so much
>
> Xueqin
>
> The error report is as follows:
> Traceback (most recent call last):
> File "/home/pxq/software/amber10/exe/MMPBSA.py", line 1376, in ?
> debug, numframes, one_trajectory)
> File "/home/pxq/software/amber10/src/mmpbsa_py/utils.py", line 1117, in gboutput
> bonddif[x] = bonddif[x] - bond[x]
> IndexError: list index out of range
>
> The FINAL_RESULTS_MMPBSA.dat is
> | Run on Fri Jan 15 16:14:44 CST 2010
> Input file:
> --------------------------------------------------------------
> #input file for running PB and GB in serial
> | Run on Fri Jan 15 16:14:44 CST 2010
> Input file:
> --------------------------------------------------------------
> #input file for running PB and GB in serial
> &general
> startframe=1, endframe=5, interval=1,
> initial_traj=1,
> complex_prmtop='3eml-zma-pop.prmtop',
> receptor_prmtop='3eml-pop.prmtop', ligand_prmtop='zma.prmtop',
> receptor_mask=':1-308 310-516', ligand_mask=':309',
try changing receptor_mask to ':1-308:310-516' (replace the space with
a colon). Does that work?
> verbose=2,
> mpi_cmd='mpirun -np 4', nproc=4
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100,
> #/
> #&pb
> # istrng=0.100,
> /
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 Fri Jan 15 2010 - 01:00:03 PST
