Hi,
Babel is working overtime since your file contains many problems:
1. dos line terminators:
.<TRIPOS>MOLECULE^M
2. nonprintable characters, which are not valid in mol2 data lines:
1 CHA 39.2040 85.2550 32.3600 C.3 ^X^F 401 BPH 0.000000^M
3. atom names containing whitespace, which are not valid mol2 atom names:
70 N A 12.6350 85.1070 25.2820 N.3 ^X^F 402 BPH 0.000000
4. something wrong with the substructure section which is causing leap
to crash:
.<TRIPOS>SUBSTRUCTURE
1 **** 1 TEMP 0 **** **** 0 ROOT
LeAP should be more robust, and I'll file a bug report.
But I recommend examining the Babel output carefully.
Scott
http://www.tripos.com/mol2/mol2_format2.html#787
On Tue, 27 Mar 2007, David LeBard wrote:
> Thank you everyone for the help and suggestions. In particular, I would
> like to thank Dr. Steinbrecher, who's suggestion worked like a charm!
>
> On 3/27/07, Thomas Steinbrecher <steinbrt.scripps.edu> wrote:
> >
> > >> I am having a problem with the loadMol2 command in xleap from Amber
> > version
> > >> 9. Basically, when I try to load a molecule from a mol2 file
> > (generated by
> > >> VMD), I get no errors but the unit is not created. So, whenever I do
> > an
> > >> edit, desc, or check on my unit, xleap says my molecule doesn't exist.
> >
> > just one suggestion, what I normally do when different programs do not
> > like structure files created by other ones is, use babel to read
> > it in and write it out again in the same format.
> >
> > Babel is quite tolerant of format inaccuracies and normally gives files
> > that all amber programs will eat without complaining.
> >
> > You can get babel at sourceforge.net I think and all you would need to do
> > is
> >
> > babel -imol2 <file> -omol2 <new_file>
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Received on Wed Mar 28 2007 - 06:07:46 PDT
