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',
verbose=2,
mpi_cmd='mpirun -np 4', nproc=4
# entropy=1,
/
&gb
igb=2, saltcon=0.100,
#/
#&pb
# istrng=0.100,
/
--------------------------------------------------------------
Complex topology file: 3eml-zma-pop.prmtop
Receptor topology file: 3eml-pop.prmtop
Ligand topology file: zma.prmtop
Initial mdcrd(s): 3eml-zma-pop.mdcrd.gz
Calculations performed using 5 frames.
All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
--- 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3:50
Hello,
If you wish to use the stripped prmtop, then you must set the variable
initial_traj=1 in your input file. This will tell the script not to
try and strip the waters itself. Then, there is no need for
solvated_prmtop, and the simulation should finish.
However, I would check the resulting mdcrds and prmtops carefully to
make sure that they are compatible. You can do this simply by loading
them into a visualization program, such as pymol or vmd.
Good luck!
Jason
On Fri, Jan 15, 2010 at 2:32 AM, xueqin pang <pangxueqintea.yahoo.com.cn> wrote:
> Hello everyone,
>
> Sorry for not providing enough information in the former e-mail. Here are some detailed information on this problem.
>
> After stripping water molecules for mdcrd files, mm-pbsa.pl can work smoothly.
>
> But it does not work well with MMPBSA.py on this the same system, I mean the same prmtops. Since according to the tutorial MMPBSA.py uses solvated mdcrd, I use the original mdcrd here. ( The original mdcrd was transformed by ptraj form a namd dcd file).
> And I do get a FINAL_RESULTS_MMPBSA.dat
>
> I have also tested the water molecular stripped mdcrd, and without solvated_prmtop. And it does not work of cause.
>
> If any other important information is miss provide here, please e-mail me.
>
> Thanks so much for you help
>
> Pang Xueqin
>
> DICP CAS
>
> The error report is as follow:
> Error: Sander output is missing values!
> VDWAALS = ************* EEL = -5847.6661 EGB = -6683.3813
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
>
> The FINAL_RESULTS_MMPBSA.dat is
> #input file for running PB and GB in serial
> | Run on Fri Jan 15 11:32:30 CST 2010
> Input file:
> --------------------------------------------------------------
> #input file for running PB and GB in serial
> &general
> startframe=1, endframe=5, interval=1,
> solvated_prmtop='E169-A-solvated.prmtop', complex_prmtop='E169-A.prmtop',
> receptor_prmtop='E169.prmtop', ligand_prmtop='A.prmtop',
> receptor_mask=':1-308', ligand_mask=':309',
> verbose=2,
> mpi_cmd='mpirun -np 4', nproc=4
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100,
> #/
> #&pb
> # istrng=0.100,
> /
> --------------------------------------------------------------
> Solvated complex topology file: E169-A-solvated.prmtop
> Complex topology file: E169-A.prmtop
> Receptor topology file: E169.prmtop
> Ligand topology file: A.prmtop
> Initial mdcrd(s): E169-A-pbsa100.mdcrd.gz
> Calculations performed using 5 frames.
> All units are reported in kcal/mole.
> -------------------------------------------------------------------------------
> -------------------------------------------------------------------------------
>
> --- 10年1月15日，周五, xueqin pang <pangxueqintea.yahoo.com.cn> 写道：
>
>
> 发件人: xueqin pang <pangxueqintea.yahoo.com.cn>
> 主题: [AMBER] problem with MMPBSA.py
> 收件人: "amber mail list" <amber.ambermd.org>, "mmpbsa.amber.gmail.com" <mmpbsa.amber.gmail.com>
> 日期: 2010年1月15日,周五,上午11:50
>
>
> Hello everyone,
>
> The problem about no bond vdwaals and 1-4VDW values in mm-pbsa calculation has already solved.
>
> I wandering can mm-pbsa.pl run in parallel form?
>
> After test MMPBSA.py test, I run it with my own system but still did not get vdwaals and 1-4VDW values while it is OK with mm-pbsa.pl. Do you have any suggestions on this problem?
>
> Thanks so much for your help
>
> Xueqin
>
> Following is my MMPBSA.py input:
> ###################################################################
> #input file for running PB and GB in serial
> &general
> startframe=1, endframe=5, interval=1,
> solvated_prmtop='E169-A-solvated.prmtop', complex_prmtop='E169-A.prmtop',
> receptor_prmtop='E169.prmtop', ligand_prmtop='A.prmtop',
> receptor_mask=':1-308', ligand_mask=':309',
> verbose=2,
> mpi_cmd='mpirun -np 4', nproc=4
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100,
> #/
> #&pb
> # istrng=0.100,
> /
>
>
> ___________________________________________________________
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>
>
>
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--
---------------------------------------
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 - 00:30:02 PST
