Re: [AMBER] Error when running

From: Bill Miller III <>
Date: Wed, 24 Nov 2010 14:09:12 -0500

Your topology files are not compatible with the trajectory (or trajectories)
you provided. You should try visualizing the trajectory your topology files.
Some possibilities might include providing a solvated trajectory with an
unsolvated topology file or vice versa. should be able to guess
the receptor and ligand masks if the residue definitions you provided are
accurate, which means the topology files are in some way incompatible with
the trajectory file you provided.

Good luck!


On Wed, Nov 24, 2010 at 12:20 PM, bin wang <> wrote:

> Dear Amber users,
> I installed MMPBSA successfully, then calculated the binding energy of a
> protein-DNA system without any problem. Now I am trying an
> antigen-antibody
> system, but got this error massage:
> ptraj found! Using /usr/local/amber10/exe/ptraj
> sander found! Using /usr/local/amber10/exe/sander
> Assuming /usr/local/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...
> Error! Ptraj failed. Check coordinate and topology files for the complex.
> NOTE: All files have been retained for debugging purposes. Type
> --clean to erase these files.
> I tried to add mask for the receptor and ligand:
> receptor_mask=':530-1435', ligand_mask=':1-529',
> But still got the same error.
> What should I do to figure out the problem? Thank you very much.
> Bin
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Wed Nov 24 2010 - 11:30:03 PST
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