AMBER Archive (2009)

Subject: [AMBER] bad atom type in mm_pbsa calculation. How to solve it? Thanks!

From: Haizhen Zhong (hzhong_at_mail.unomaha.edu)
Date: Wed Jun 03 2009 - 18:00:34 CDT

   Dear AMBER users,
   I am trying to run an mm_pbsa calculatio This ligand contains a Bromine atom, atom types (br, according to gaff.dat) an simulations proceeded very well for both l mm_pbsa tutorials on the amber webs ligand, receptor, and complex, which went However, when I tried to calculate the binding energy, command,
   ./mm_pbsa.pl energy_binding_mm_gbsa it returned
   bad atom type: br
   /opt sander_com.1.out -c ./RV1_0320_2000_cpx.prmtop not successful. The prmtop was for the cpx (complex) was generated in xleap using t snapshot at 2000ps, with prepin and frcmod of bromine-containing ligand imported, the saveamberparm command indicated the prmtop files were generat ed properly.
   Any suggestion to solve this problem?
   Thank you Andy Zhong

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