[AMBER] GBSA error

From: jacob wick <jacobwick.la.gmail.com>
Date: Wed, 12 Dec 2018 11:15:32 +0530

---------- Forwarded message ----------
From: *jacob wick* <jacobwick.la.gmail.com>
Date: Tuesday, December 11, 2018
Subject: GBSA error
To: AMBER Mailing List <amber.ambermd.org>

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

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:


  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
   startframe=1, interval= 25, endframe=1000, strip_mask=":WAT"
  igb=2, saltcon=0.0
  idecomp=1, print_res="44; 144-149; 168-172"

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

Thanks and Regards,
AMBER mailing list
Received on Tue Dec 11 2018 - 22:00:02 PST
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