Thank you Jason for the reply.
After checking the spaces at "/" as well as checking the compatibility of the topology files, the mmpbsa.py finished the job. The problem I face now is the 'segfault' error from sander9 when it calculates the ligand coordinates (which in this case is a peptide with 12 residues).
The lsf.out show:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander 00000000004304C0 Unknown Unknown Unknown
sander 0000000000734566 Unknown Unknown Unknown
sander 00000000004B076B Unknown Unknown Unknown
sander 00000000004A3935 Unknown Unknown Unknown
sander 00000000004A10E6 Unknown Unknown Unknown
sander 000000000049C928 Unknown Unknown Unknown
sander 00000000004038AA Unknown Unknown Unknown
libc.so.6 0000003FAFC1C3FB Unknown Unknown Unknown
sander 00000000004037EA Unknown Unknown Unknown
When I checked the output file:
| Run on Tue Jul 20 17:17:32 SGT 2010
|Input file:
|--------------------------------------------------------------
|MMPBSA.py input file for running GB
|&general
| startframe=5000, endframe=5050,
| verbose=2, interval=1, strip_mdcrd=1,
|# entropy=1,
|/
|&gb
| igb=2, saltcon=0.0072
|/
|--------------------------------------------------------------
|Complex topology file: ./ABC.prmtop
|Receptor topology file: ./AC.prmtop
|Ligand topology file: ./B.prmtop
|Initial mdcrd(s): ./complex.mdcrd
|
|Best guess for receptor mask: ":1-187:200"
|Best guess for ligand mask: ":188-199"
|Calculations performed using 51 frames.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
~
The input file generated by the mmpbsa.py shows:
------------------------------------
Here is the input file:
File generated by MMPBSA.py
&cntrl
ntb=0, idecomp=0, cut=999.0, nsnb=99999,
imin=5, maxcyc=0, ncyc=0, igb=2,
saltcon=0.0072, intdiel=1, extdiel=78.3,
gbsa=2, surften=0.0072,
/
--------------------------------------------
I do not think there is an error from this input file generated by mmpbsa.py.
Next, I checked the *complex_gb.mdout file:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 4.1603E+11 2.0384E+11 1.3011E+13 CB 977
BOND = ************* ANGLE = 373559.8688 DIHED = 10267.5296
VDWAALS = ************* EEL = -913.1742 EGB = -28522.9796
1-4 VDW = 3271043.7734 1-4 EEL = -66.7265 RESTRAINT = 0.0000
ESURF = 830.3698
minimization completed, ENE= 0.41603215E+12 RMS= 0.203844E+12
minimizing coord set # 3
The program sander was not able to calculate the BOND and VDWAALS terms. Why ? The values of the other terms are quite big ! For the *receptor_gb.mdout and *ligand_gb.mdout, values are strangely the same as above.
Could it be that the something wrong happened during the generation of snapshots? But as one can see in the output file, the mmpbsa.py automatic guesser was able to guess or assign correctly the receptor and ligand. When I viewed by vmd the *_avgcomplex.pdb file shows erratic with bonds broken all over upside down !
I am at lost here. If the only cause of the problem is segmentation fault, even I issued a command at console for 'ulimit -s unlimited' it didnt have any effect. And since the generated snapshots were incorrect, how to fix it knowing mmpbsa.py has assigned well the ligands, receptor.
Please be patient to this post ! I believe that the solution is out there. Thanks a lot for taking time.
Amor
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Received on Tue Jul 20 2010 - 03:30:03 PDT
