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
Received on Wed Sep 27 2017 - 09:00:02 PDT
