Re: [AMBER] AddtoBox failure

From: David Case <>
Date: Tue, 2 May 2017 21:24:55 -0400

On Tue, May 02, 2017, sylvester kisembo wrote:

> Has anyone had trouble recently getting AddtoBox to work in Ambertools 16/17?
> I have tried this command on my machine and on the super computer:
> AddToBox -c start.pdb -a input.pdb -na 7 -o combo.pdb -P 26 -RP 3.0 -RW
> 6.0 -G 0.2 -V 1

I use it all the time...from your output, it looks like the path for
recursive calls may not be correct. Type "AddToBox" with no arguments to
see the options. Make sure that your AMBERHOME variable is correctly set,
and that AddToBox is actually in $AMBERHOME/bin.

I'm not sure what is in "input.pdb", but assinging a relativel large radius
of 6 Ang. might be a problem. Have you tried smaller radii?

> But i never get any molecules added even after recursive tries. This is always the result:
> AddToBox >> Added 0 residues.
> AddToBox >> Residue goal not achieved.
> AddToBox >> Re-attempting with solvent clipping radius   4.3740.
> GetPDB >> Found 26 atoms in combo.pdb.
> GetPDB >> Bracketed 1 residues.
> GetPDB >> Found 26 atoms in L.pdb.
> GetPDB >> Bracketed 1 residues

Can you post the full output? You may need to provide the files and the
actual command line you used. (Note that the program refers to "L.pdb",
whereas the command line above has no such file.)


AMBER mailing list
Received on Tue May 02 2017 - 18:30:02 PDT
Custom Search