Re: [AMBER] Re: Error: No potential terms in sander output!

From: Jim Paugh <>
Date: Wed, 02 Jun 2010 05:30:53 -0700 (PDT)

-----Original Message-----
From: Bill Miller III <>
Date: Wednesday, Jun 2, 2010 6:48 am
Subject: [AMBER] Re: Error: No potential terms in sander output!
To: vaibhav dixit <>
CC: AMBER Mailing List <>Reply-To: AMBER Mailing List <>

Your ligand is just one residue, right? If this is the case, then should be able to guess the receptor_mask and ligand_mask without you specifying it. If cannot guess the masks with a one residue ligand, then more than likely there is an inconsistency with the prmtop files.

The error that you are now getting means that the sander calculations (GB and PB) did not actually calculate any energies. The reason for this error is probably a sander error that should be near the end of the
_MMPBSA_*.mdout files. This should have a sander error message that will be helpful. You also might want to check the STDOUT and STDERR files for any possibly important messages that got printed there.

Good luck!


On Wed, Jun 2, 2010 at 6:37 AM, vaibhav dixit <>wrote:

> Dear Amber community member,
 Thanks for your suggestions earlier.
 I have tried to fix the receptor and ligand masking issue as specified in
 the mail below. Please check if thats ok.

> But now I'm getting another error as follows. I'm not able to understand
 what is this potential terms error in sander output. I have attached my
 initial and avgcomplex pdb files here, but can't attach the mdcrd file as
 it makes the message large and is not delivered.

> Please find time and see if you can suggest some solution to the issue.

> The ERROR is given below.
 [vaibhav.localhost MMPBSA]$ pwd
 [vaibhav.localhost MMPBSA]$ $AMBERHOME/bin/ -O -i mmpbsa_2b.inFINAL_RESULTS_MMPBSA.dat -sp 2PRG_rosi_solvated.prmtop -cp
 2PRG_rosi_NW.prmtop -rp 2PRG_nolig.prmtop -lp rosi.prmtop -y *.mdcrd
 ptraj found! Using /home/vaibhav/software/amber10/exe/ptraj
 sander found! Using /home/vaibhav/software/amber10/exe/sander (serial
 Assuming /home/vaibhav/software/amber10/exe/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...
 50 frames were read in and processed by ptraj for use in calculation.

> Starting sander calls

> Starting gb calculation...

> Starting pb calculation...

> Error: No potential terms in sander output! Check output files.
 NOTE: All files have been retained for debugging purposes. Type
 --clean to erase these files.

AMBER mailing list
Received on Wed Jun 02 2010 - 06:00:14 PDT
Custom Search