Hey,
in my setup of things, MMPBSA.py writes a "RES EDIT" to an mdin file,
while `EDIT` could have been replaced by the entire residue range,
because I did not specify `print_res`. This is what I have done:
My ligand consists of residues 1-106 and residues 312-355. My receptor
consists of residues 107-311.
1) ante-MMPBSA
==============
$ ante-MMPBSA.py -p ../topology.top -c ../initcoords.crd -cp
complex_unsolvated.prmtop -rp receptor.prmtop -lp ligand.prmtop
-strip_mask ":WAT" -receptor_mask ":107-311"
[output attached, there are several warnings that I am worried about,
but should be unrelated to the problem discussed here]
2) MMPBSA input file
====================
&general
startframe = 1000,
endframe = 1020,
interval = 5,
receptor_mask = :107-311,
ligand_mask = :1-106,312-355
/
&gb
igb = 5,
/
&decomp
idecomp = 1,
dec_verbose = 3,
/
3) MMPBSA.py to create mdin files
=================================
$ MMPBSA -i mmpbsa_decomp.in -cp complex_unsolvated.prmtop -sp
../topology.top -rp receptor.prmtop -lp ligand.prmtop -y
../md_equilibrate_00*
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
Warning: Problem parsing L-J 6-12 parameters.
ptraj found! Using /home/bioinfp/jang/apps/amber11/bin/ptraj
sander found! Using /apps11/bioinfp/amber10+/bin/sander for GB calculations
Warning: Decomposition is only automated if I guess the ligand and receptor
masks! I will write skeleton mdin files which you must edit. Re-run
MMPBSA.py with -use-mdins, or allow me to guess the masks.
4) MMPBSA.py running sander
===========================
MMPBSA -i mmpbsa_decomp.in -cp complex_unsolvated.prmtop -sp
../topology.top -rp receptor.prmtop -lp ligand.prmtop -use-mdins -y
../md_equilibrate_00*
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
Warning: Problem parsing L-J 6-12 parameters.
ptraj found! Using /home/bioinfp/jang/apps/amber11/bin/ptraj
sander found! Using /apps11/bioinfp/amber10+/bin/sander for GB calculations
Preparing trajectories for simulation...
20 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
* Error from _MMPBSA_complex_gb.mdout:
> rfree: Error decoding variable 2 2 from:
>RES EDIT
>
> this indicates that your input contains
>
> incorrect information
>
> field 2 was supposed to
>
> have a (1=character, 2=integer, 3=decimal) value
* Corresponding _MMPBSA_gb_decomp_com.mdin (why don't we have a
constant name prefix for in and out files?)
> File generated by MMPBSA.py
> &cntrl
> nsnb=99999, ntb=0, surften=0.0072,
> extdiel=78.3, ncyc=0, cut=999.0,
> gbsa=2, imin=5, idecomp=1, igb=5,
> /
> Residues considered as REC
> RRES 107 311
> END
> Residues considered as LIG
> LRES 1 106,312 355
> END
> Residues to print
> RES EDIT
> END
> END
Is this intended behavior by MMPBSA.py? Most probably the `EDIT` could
have been set by MMPBSA.py automatically to the entire residue range (as
I did not specify `print_res` in the MMPBSA input file). After doing
this manually, sander/MMPBSA.py runs smoothly.
Jan-Philip
--
Jan-Philip Gehrcke
PhD student
Structural Bioinformatics Group
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
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Received on Wed Oct 05 2011 - 08:00:03 PDT
