There is a small error in the manual about strip_mdcrd. it should be =0 if
you do not want to strip out the water. I guess this is your case as you do
not use -sp. I think this could be the cause of your problems. These errors
usually mean problems with the top files matching the crd file.
All the best,
Oliver
On 20 July 2010 11:16, Amor San Juan <amorsanjuan.yahoo.com> wrote:
> 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 - 04:00:03 PDT
