Dear Amber users,
I want to calculate the binding free energy of a protein-protein complex.
My complex contains metals which I have stripped before MMPBSA calculations.
I used ante-MMPBSA to create the receptor and ligand prmtops from the
complex prmtop. I also generated a stripped binpos trajectory with 101
frames for MMPBSA.
I used the stripped prmtop and stripped binpos to calculate RMSD using
cpptraj to check the compatibility and it worked out fine. The cpptraj
reads all 101 frames and calculates RMSD.
I am using AmberTools 14 (update 3). I have previously performed MMPBSA for
many protein complexes without any errors.
My input file is:
Sample input file
&general
verbose=2, keep_files=1,
/
&gb
igb=5,
/
But for this complex I am getting the following error:
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/amber/amber14/bin/mmpbsa_py_energy
cpptraj found! Using /opt/amber/amber14/bin/cpptraj
Preparing trajectories for simulation...
TrajError: start frame (1) > total frames (0)
Exiting. All files have been retained.
This error occurs for both serial and parallel runs.
when the same complex is run in AmberTools 12, i get a "memory corruption"
error.
if i use "use_sander = 1", the complex alone runs fine and .mdout is
created, but when shifting to receptor, the program fails with an error
"invalid next read".
I have tried several runs by creating new prmtops, using sander, with
netcdf/mdcrd/binpos trajectories but the error persists.
The temporary pdb and mdcrd files are generated properly but the MMPBSA
calculations doesn't start due to the error.
What may cause this error and how to solve this?
Thank you,
With regards,
B. Sangeetha
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Received on Tue Sep 01 2015 - 09:00:04 PDT
