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,
/
___________________________________________________________
好玩贺卡等你发，邮箱贺卡全新上线！
http://card.mail.cn.yahoo.com/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 15 2010 - 00:00:02 PST
