[AMBER] GBSA error

From: jacob wick <jacobwick.la.gmail.com>
Date: Tue, 11 Dec 2018 14:19:15 +0530

Dear all,

I am using the following input file and generated the dry top for complex
protein and drug using both methods: 1) pdb file (tleap) and 2) trajectory
(ante-MMPBSA.py)

Still the error in LOG file shows:

CalcError: /opt/apps/amber14/bin/cpptraj failed with prmtop drydock.top!

and the last file generated is _MMPBSA_complex_gb.mdout.0 with last line as:

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

  FATAL: NATOM mismatch in coord and topology files



whereas the number of atoms and format of top and crd both are correct.
No. of atoms in Complex Dry: 3506
No. of atoms in Protein: 3427
No. of atoms in Ligand: 79
With box complex: 90751 atoms

Also, I am able to generate pdbs from the individual frames and able to
visualize the trajectory using the box top file correctly. I am also able
to generate pdb using the drydock.top and drydock.crd via ambpdb. All the
files show complete pdb without any error.


Input file for running GB
&general
   startframe=1, interval= 25, endframe=1000, strip_mask=":WAT"
/
&gb
  igb=2, saltcon=0.0
/
&decomp
  idecomp=1, print_res="44; 144-149; 168-172"
  dec_verbose=1,
/

Pl. guide what could be the possible reason for the error.

Thanks and Regards,
Jac
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Received on Tue Dec 11 2018 - 01:00:02 PST
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