This is actually a fairly common message with MM-PBSA calculations with
Amber. If you google for MMPBSA.py and "bad atom type: Br" you will get a
lot of responses on the Amber list with suggested fixes. For example:
http://archive.ambermd.org/201111/0370.html
Good luck!
-Bill
On Thu, Mar 5, 2015 at 6:26 AM, Emilio Angelina <
emilioluisangelina.hotmail.com> wrote:
> 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
> Emilio
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Post-doc
University of Richmond
417-549-0952
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 05 2015 - 07:30:02 PST
