MM-PBSA query

[Viswanath Vittaladevaram]

Hi,

I tried doing MM-PBSA analysis and I found this in my log file

Loading and checking parameter files for compatibility...
CHAMBER prmtops found. Forcing use of sander
sander found! Using /ichec/packages/amber/18/bin/sander
cpptraj found! Using /ichec/packages/amber/18/bin/cpptraj
Preparing trajectories for simulation...

What could be the mistake here?

Regards,

Viswanath.V

[Mario Sergio Valdes]

There is no error. In previous versions, the calculation could be carried out using mmpbsa_py_energy or sander. mmpbsa_py_energy doesn't support charmm-derived topology, so we were forced to use sander for the calculation. 

In the latest versions, sander is always used, so this warning can be omitted.

[Viswanath Vittaladevaram]

Hi ,

I need help on this error.

Here is mm-pbsa.sh script

warnings.warn('receptor_mask overwritten with default\n')

/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/main.py:603: Us

erWarning: receptor_mask overwritten with default

  warnings.warn('receptor_mask overwritten with default\n')

  File "/ichec/packages/amber/18/bin/MMPBSA.py.MPI", line 99, in <module>

    app.file_setup()

  File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 141, in file_setup

    create_inputs(INPUT, self.normal_system, self.pre)

  File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/createinput.py", line 56, in create_inputs

    com_card, rc_card, lc_card = prmtop_system.Group(INPUT['print_res'],True)

  File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py", line 541, in Group

    rec_group_type, lig_group_type)

  File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py", line 591, in _binding_group

    self._select_residues(selection)

  File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py", line 834, in _select_residues

    raise SelectionError('Invalid selection. Illegal residue range')

Pbsa.in file details are below

And find pbsa.log file details below

Sample input file for MM-PBSA calculation

&general

    startframe=1, endframe=3, interval=1,

    strip_mask=:SOL:WAT:CL:CIO:CS:IB:K:LI:MG:NA:RB:Na+:Cl-,

    verbose=2, keep_files=1,

    receptor_mask=:1-271,

    #ligand_mask=:272-,

/

&pb

    indi=1, exdi=80, inp=1, radiopt=0,

    fillratio=4.0, istrng=0.15,

    linit=1000, prbrad=1.4, scale=2.0,

    cavity_surften=0.0378, cavity_offset=-0.5692,

/

&decomp

  idecomp=1, print_res="1-271;1-271,272-1316"

  dec_verbose=1, csv_format=0

/

pbsa.in (END)

Pbsa.log file shows as follows

Loading and checking parameter files for compatibility...

CHAMBER prmtops found. Forcing use of sander

sander found! Using /ichec/packages/amber/18/bin/sander

cpptraj found! Using /ichec/packages/amber/18/bin/cpptraj

[Mario E. Valdes-Tresanco]

Looks like you are using MMPBSA.py... This group is intended to provide support for gmx_MMPBSA... please post this error in the amber mailing list, they might be of better help

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