RE: AMBER: Sander Error

From: Ross Walker <>
Date: Fri, 29 Jun 2007 20:42:50 -0700

> We are trying to minimize 5 ligands in protein . The minimization in
> SANDER works for just the protein but when we run SANDER with the
> ligands we get this error

> The system has extended beyond
> the extent of the virtual box.

> &cntrl
> imin = 1,
> maxcyc = 500,
> ncyc = 250,
> ntb = 0,
> igb = 0,
> cut = 12
> /

If this is happening during minimization then it should tell you that
something is very very wrong with your starting structure. Do you really
expect an atom to move by 30 angstroms during minimization? Take a careful
look at the actual output, I bet you have some huge energy and consequently
a huge force. Look at the RMS and GMAX entries and in particular the atom
number of the atom with the maximum force that is printed. Then visualy
inspect your starting structure and then perhaps you will see the problem.

In addition are you certain you want a gas phase minimum? If so then fine
but you have to realize that there is no reason why your protein and ligand
should actually be stable in a vacuum... This is an aside however, firstly
you need to fix the structural defects in your starting structure. If you
can't find anything wrong here then carefully check the parameters you are
using - do you have some equilibrium bond length set to some crazy long

Good luck...


|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Sun Jul 01 2007 - 06:07:41 PDT
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