AMBER Archive (2004)

Subject: Re: AMBER: Loading mol2 Files in XLEaP

From: Robyn Ayscue (kajsicat_at_yahoo.com)
Date: Fri Jun 04 2004 - 13:24:05 CDT

Hi! I finally got it sorted out. It wasn't Amber
itself, but a problem with my .cshrc file. It was
sourcing an outdated amberrc file and that was the
root of the problem. I did have a .pdb file (built by
Sybyl), but I was interested in a DNA oligo with a
modified base, and XLEaP didn't recognize the
modification when I'd try to load the .pdb. It
recognised the .pdb (also built by Sybyl) of the
unmodified, canonical oligo, with the exception of the
terminal bases. Now that I've fixed my .cshrc file,
XLEaP recognizes the mol2 file, AND the modified
base, thankfully.

Again, thanks for all your help!

Yours,
Robyn Ayscue

--- FyD <fyd_at_u-picardie.fr> wrote:
> Quoting Robyn Ayscue <kajsicat_at_yahoo.com>:
>
> > Thanks for your help. I checked the mol2 files I
> have
> > and they all contain the @<TRIPOS>SUBSTRUCTURE
> tag.
> > The "Syntax error" I keep getting sounds like
> XLEaP
> > doesn't like they way I'm entering the command,
> but
> > I've typed it verbatim to what you provided in
> your
> > example, which is the same as what's in the
> manual.
> > Does anything other than mis-typed commands
> provoke a
> > "syntax error" in XLEaP?
>
> I do not know.
>
> Did you try to load a PDB file instead of a Tripos
> file in xleap. Do you have
> the same problem ?
>
> M = loadpdb M.pdb
>
> Can you send me your Tripos file ? I could try it on
> my system.
>
> Regards, Francois
>
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