Re: [AMBER] MMPBSA failed

From: Albert <>
Date: Tue, 31 Jan 2017 16:41:15 +0100

I add this option in the as following:

    endframe=100, verbose=1, use_sander=1
   igb=2, saltcon=0.150
   istrng=0.150, fillratio=4.0

unfortunately it failed with similar errors:

> -O -i -o FINAL_RESULTS_MMPBSA.dat -sp
sol.prmtop -cp com.prmtop -rp rec.prmtop -lp lig.prmtop -y prod*.mdcrd

Loading and checking parameter files for compatibility...
sander found! Using /home/albert/install/amber16/bin/sander
cpptraj found! Using /home/albert/install/amber16/bin/cpptraj

Preparing trajectories for simulation...
100 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /home/albert/install/amber16/bin/sander
   calculating complex contribution...
   File "/home/albert/install/amber16/bin/", line 100, in <module>
line 218, in run_mmpbsa, self.stdout)
line 82, in run, stdout=stdout, stderr=stderr)
line 157, in run
CalcError: /home/albert/install/amber16/bin/sander failed with prmtop
Exiting. All files have been retained.

On 01/31/2017 04:07 PM, Vlad Cojocaru wrote:
> Please look in the manual at how to run MMBPSA ... There is a keyword
> that allows you to instruct the script to use sander ....

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Received on Tue Jan 31 2017 - 08:00:02 PST
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