AMBER Archive (2009)


From: case (
Date: Fri Sep 18 2009 - 08:26:40 CDT

On Fri, Sep 18, 2009, Silvia Carlotto wrote:
> I have a problem with the CHCL3BOX
> then I save the pdb
> savepdb CHCL3BOX box.pdb
> but if I load with xleap this file with
> P=loadpdb box.pdb

Unfortunately, this won't work with the stock release, because the standard
datbase contains no "CL3" residue that corresponds to a single chloroform

The straightforward "solution" is to create such a unit, probably by editing
the file (in $AMBERHOME/dat/leap/lib), and saving it under a new
name, then loading that.

However, are you sure you need to do this? The reason that no such unit is
around is that it usually is not needed. You can use the chloroform in the
usual way, by using it to solvate some solvent, then using saveAmberParm.
Under the most common circumstances, it should not be necessary to create
a pdb file and load that into LEaP. So, be sure you really need to work with
the box.pdb file before going down the path outlined in the previous

...good luck...dac

AMBER mailing list