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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--
---------------------------------------
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 - 00:00:03 PST
