[AMBER] error in MMPBSA.py

From: Emilio Angelina <emilioluisangelina.hotmail.com>
Date: Thu, 5 Mar 2015 11:26:43 +0000

Dear AMBER users

I am trying to run a mm-gbsa calculation for a proteing-ligand comples where the ligand has a bromine atom plus an extra-point at the top of the bromine. I got the following error. Does this issue might be related with the extra-point ?

MMPBSA.py -O -i mmpbsa_d.in -o FINAL_RESULTS_MMPBSA.dat -sp D2h_halo-Br-EP_solvated.top -cp D2h_halo-Br-EP.top -rp D2h.top -lp halo-Br-EP.top -y ../../md/md_1.trj
Loading and checking parameter files for compatibility...
sander found! Using /home/angelina-asus/amber/bin/sander
cpptraj found! Using /home/angelina-asus/amber/bin/cpptraj
Preparing trajectories for simulation...
1 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /home/angelina-asus/amber/bin/sander
  calculating complex contribution...
 bad atom type: br
CalcError: /home/angelina-asus/amber/bin/sander failed with prmtop D2h_halo-Br-EP.top!
Exiting. All files have been retained.

Thanks in advance
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Received on Thu Mar 05 2015 - 03:30:02 PST
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