[AMBER] MMPBSA.py calculations...bad atom type

From: RANAJIT SHINDE <science.ranajitshinde.gmail.com>
Date: Sat, 5 Jun 2010 11:14:23 +0530

Dear all,

We have amber10 and MMPBSA.py installed on CentOS. I am running mmpbsa
calculations for the enzyme-inhibitor complex where inhibitor has the
“bromine” atoms. After running the following command,

$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
complex_sol.prmtop -cp complex_vac.prmtop -rp protein.prmtop -lp
ligand.prmtop -y *.mdcrd

calculations proceeded as this,

ptraj found! Using /opt/amber10/bin/ptraj

sander found! Using /opt/amber10/bin/sander

Assuming /opt/amber10/bin/sander is part of

amber9 or amber10. Using old PB input file.

Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified
Bondi radii (mbondi)

Preparing trajectories with ptraj...

5 frames were read in and processed by ptraj for use in calculation.

Starting calculations...

Starting gb calculation...

  calculating ligand contribution...

 bad atom type: br

  calculating receptor contribution...

  calculating complex contribution...

 bad atom type: br

Starting pb calculation...

  calculating ligand contribution...

  calculating receptor contribution...

  calculating complex contribution...

Calculations complete. Writing output file(s)...

Error: No potential terms in sander output! Check output files.

NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.

It encountered two problems. 1. bad atom type br and 2. Potential term.

So could you please tell how to fix the bad atom type? Is there any file
which can be modified with atom types (like mm_pbsa_calceneent.pm in case of

Is the problem of halogen atoms for mmpbsa calculation is taken care in

How to fix the error “no potential terms in sander output”?

I am attaching FINAL_RESULTS_MMPBSA.dat file for the information.

Kindly assist

Ranajit Shinde
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Received on Fri Jun 04 2010 - 23:00:03 PDT
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