AMBER Archive (2004)

Subject: Re: AMBER: Box information from Amber

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sat Oct 09 2004 - 07:10:56 CDT

we need more info to help-
are you using iwrap? if not, molecules may move out of the box (which
is fine, the image molecules move in)

also, where is the box in "amber pdbs", I wasn't aware that the pdb format
fles that amber writes have box coordinates, maybe they do.

are the furtherst atoms in a straight line along 1 axis? distances along
the diagonal of the box can be longer.

please be detailed- tell us which files, which amber version, and your
input file.

carlos

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Priti Hansia wrote:

>Hi all,
>
>I have simulated a protein with 326 residues and around 15000 water
>molecules. The box information which I get from amber PDBs does not match
>with the box infromation given in crd or en files. For example, the box
>size for a particular snapshot is 73.87 76.38 86.45 from crd files, but
>the distance between two furthest atoms is seen to be around 120 angstrom.
>Can you please help me out of this problem ?
>
>Thanks,
>-Priti.
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