AMBER Archive (2003)

Subject: Re: how to stop mapping of N- and C-terminal residues in xleap (The RTFM solution)

From: Michael Ford (mford_at_ccrc.uga.edu)
Date: Wed Jan 15 2003 - 12:02:52 CST

Thanks to everyone who weighed in on this. The answer (I must admit
sheepishly is in the manual) is the -s in the xleap call which supresses the
calling of leaprc.

Thanks again,

Mike Ford

Vlad Cojocaru wrote:

> You have to change the xleap (from ${AMBERHOME}/exe) startup script,
> move it somewhere else and add there the path of your modified leaprc,
> because otherwise it will always load the default leaprc.
> Hope this help,
> vlad
>
> Michael Ford wrote:
>
> >Hello,
> >
> >I need to know how to stop the mapping of N- and C-terminal residues by
> >xleap. What I mean is that there are statements in the leaprc file such
> >as:
> >
> >addPdbResMap {{ 0 "ALA" "NALA}.......}
> >
> >I can remove these statements from a local version of the leaprc file,
> >and then source that file, but the residues keep getting mapped back to
> >the N- and C-terminal versions. I assume that xleap is sourcing some
> >other version of this file, which I can't seem to track down. I've also
> >tried to remove the atoms, but then I get into a big xleap mess.
> >
> >Any help is appreciated,
> >
> >Mike Ford
> >
> >
> >
>
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1389
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> home tel: ++49-551-9963204