Hi,
You need to make sure you're using the xleap from amber8.
Guanglei
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?
>
> Yours,
> Robyn Ayscue
>
> --- 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...
>>
>>Regards, Francois
>>
>>F.-Y. Dupradeau
>> --
>>The Scripps Research Institute, San Diego, CA
>>Faculte de Pharmacie, UPJV, Amiens, France
>> --
>>http://www.u-picardie.fr/labo/lbpd/fyd.htm
>>
>
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Received on Thu Jun 03 2004 - 20:53:01 PDT
