>>>>>>>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
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>
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Received on Wed Sep 27 2017 - 10:00:02 PDT
