Hi,
On Thu, 3 Jun 2004, Robyn Ayscue wrote:
> 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?
No.
Perhaps we can roust two birdies with one nugget of amber ;-)
The first debugging principle - document the failure:
send us the ouputs from the commands
echo $AMBERHOME
which xleap
cat -e -t -v leap.log | tail
> --- FyD <fyd.u-picardie.fr> wrote:
> > Quoting Robyn Ayscue <kajsicat.yahoo.com>:
> >
> > > Hi! I'm using Amber 8 on an SGI machine running
> > Irix
> > > 6.5, and I've been having a bit of trouble with
> > xLEaP
> > > regarding the "loadmol2" command mentioned in the
> > > manual. I've tried to load a file by entering the
> > > following commands:
> > >
> > > variable = loadmol2 "test.mol2"
> > > variable = loadmol2 test.mol2
> > > loadmol2 test.mol2
> > >
> > > With each of them I get "syntax error" back from
> > the
> > > program, and the file fails to load. The file is
> > > located in the same directory I'm running the
> > program
> > > from. Also, if it makes any difference, the file
> > is a
> > > canonical B-conformation T:A 15-residue
> > > oligonucleotide (DNA). Has anyone else had this
> > > problem? If so, how did you fix it? Any help would
> > be
> > > appreciated.
> >
> > It worked for me:
> > M = loadmol2 M.mol2
> >
> > However, the section ".<TRIPOS>SUBSTRUCTURE" must be
> > present in the Tripos
> > format. See
> > http://www.tripos.com/custResources/mol2Files/
> >
> > For instance Babel does generate .mol2 file without
> > this section. If a Tripos
> > file is loaded without this section the unit created
> > stays empty...
Regardless of the contents of the mol2 file a syntax error should not occur.
For example, if mtx.mol2 is an empty file:
> m=loadmol2 mtx.mol2
Loading Mol2 file: ./mtx.mol2
> desc m
STRING (with no reference): 'm'
The ouput of the three commands should look like this:
echo $AMBERHOME
/usr/local/srb/amber/amber9
which xleap
/usr/local/srb/amber/amber9/exe/xleap
cat -e -t -v leap.log | tail
> desc MTX$
UNIT name: methotrexate$
Head atom: null$
Tail atom: null$
Contents: $
R<MTX 1>$
> m=loadmol2 mtx.mol2$
Loading Mol2 file: ./mtx.mol2$
> desc m$
STRING (with no reference): 'm'$
Scott Brozell
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Received on Thu Jun 03 2004 - 22:53:00 PDT
