---------- 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
(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 - 22:00:02 PST
