Dear Elvis,
I tried with use_sander=1 in the &general section.
The LOG file says same, however the last and the only mdout is
_MMPBSA_complex_gb.mdout.0
with the last lines as:
* FATAL: NATOM mismatch in coord and topology files*
which is not true as I checked the drycomplex had 2035 atoms and the
protein had 1989 while drug 46 had atoms in their respective top files.
So what next can you suggest.
Jac
On Wed, Sep 27, 2017 at 10:23 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> The error seems to be with the "drydocked.prmtop" file.
> I would first to use, in the &general,
> "use_sander=1" check if your calculations works.
> If it still fails then my guesses will be either it is not in the right
> path or you have not defined GB radii correctly.
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: jacob wick <jacobwick.la.gmail.com>
> Sent: 27 September 2017 22:04
> To: AMBER Mailing List
> Subject: Re: [AMBER] Error with MMGBSA/PBSA
>
> >>>>>>>If you see carefully your job has crashed with some error.
>
> Yes, but what could be the possible error and how to fix.
>
> _MMPBSA_complex_gb.mdout.0 is the only mdout created.
>
>
>
> Jac
>
> On Wed, Sep 27, 2017 at 9:58 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > HI,
> > If you see carefully your job has crashed with some error.
> > -----------------------------------------------
> > self.prmtop))*
> > *CalcError: /opt/apps/amber14/bin/cpptraj failed with prmtop
> > drydocked.prmtop!*
> > *Exiting. All files have been retained.*
> > *mmpbsa_py_energy found! Using /opt/apps/amber14/bin/mmpbsa_py_energy*
> > *cpptraj found! Using /opt/apps/amber14/bin/cpptraj*
> > -----------------------------------------------------------------
> >
> > >>>>>>>>>>>_MMPBSA_complex_gb.mdout.0 <<<<<<<<
> > Look at all the mdout files to see what has possibly gone wrong.
> > Best Regards
> > Elvis Martis
> > Mumbai, INDIA.
> >
> > ________________________________________
> > From: jacob wick <jacobwick.la.gmail.com>
> > Sent: 27 September 2017 21:08
> > To: AMBER Mailing List
> > Subject: [AMBER] Error with MMGBSA/PBSA
> >
> > Dear all,
> >
> >
> > I am using the MMGBSA/PBSA to calculate the free energy binding for a
> > protein-ligand complex using the following script
> >
> > *Input file for running PB and GB*
> > *&general*
> > * endframe=50, keep_files=2,*
> > */*
> > *&gb*
> > * igb=2, saltcon=0.100,*
> > */*
> > *&pb*
> > * istrng=0.100,*
> > */*
> >
> >
> > in LOG file following error showed:
> >
> > *-----------------------------------------------------------
> > ---------------*
> >
> > *50 frames were processed by cpptraj for use in calculation.
> >
> > *Running calculations on normal system...*
> >
> > *Beginning GB calculations with /opt/apps/amber14/bin/mmpbsa_py_energy*
> > * calculating complex contribution...*
> > * File "/opt/apps/amber14/bin/MMPBSA.py", line 96, in <module>*
> > * app.run_mmpbsa()*
> > * File "/opt/apps/amber14/bin/MMPBSA_mods/main.py", line 218, in
> > run_mmpbsa*
> > * self.calc_list.run(rank, self.stdout)*
> > * File "/opt/apps/amber14/bin/MMPBSA_mods/calculation.py", line 79, in
> > run*
> > * calc.run(rank, stdout=stdout, stderr=stderr)*
> > * File "/opt/apps/amber14/bin/MMPBSA_mods/calculation.py", line 459, in
> > run*
> > * self.prmtop))*
> > *CalcError: /opt/apps/amber14/bin/cpptraj failed with prmtop
> > drydocked.prmtop!*
> > *Exiting. All files have been retained.*
> > *mmpbsa_py_energy found! Using /opt/apps/amber14/bin/mmpbsa_py_energy*
> > *cpptraj found! Using /opt/apps/amber14/bin/cpptraj*
> >
> >
> >
> > The last file generated is _MMPBSA_complex_gb.mdout.0 and the last part
> of
> > the file says:
> >
> > *Processing frame 50*
> > * eff.c(2713) enb14 --> 476.144*
> > * eff.c(2714) eel14 --> 4945.716*
> > * eff.c(2772) enb --> -968.619*
> > * eff.c(2773) eel --> -8924.495*
> > * eff.c(2774) e_gb --> -1911.657*
> > * eff.c(2775) esurf --> 47.711*
> > * eff.c(2776) evdwnp --> 0.000*
> > * BOND = 406.2733 ANGLE = 1037.5399 DIHED =
> > 1316.0992*
> > * VDWAALS = -968.6189 EEL = -8924.4950 EGB =
> > -1911.6567*
> > * 1-4 VDW = 476.1438 1-4 EEL = 4945.7157 RESTRAINT =
> > 0.0000*
> > * ESURF = 47.7115*
> >
> > *MM/GBSA processing done!*
> >
> >
> > However, I am unable to generate the RESULT file using the following
> > command.
> >
> >
> > *MPBSA.py -O -i mmpbsa.in <http://mmpbsa.in> -o RESULT -sp docked.prmtop
> > -cp drydocked.prmtop -rp protein.prmtop -lp drug.prmtop -y prod.mdcrd
> >LOG*
> >
> >
> >
> >
> > Any suggestion what could be possibly wrong.
> >
> >
> > Jac
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Sep 28 2017 - 07:30:03 PDT
