AMBER Archive (2007)

Subject: Re: AMBER: Question about loadMol2

From: David LeBard (david.lebard_at_asu.edu)
Date: Tue Mar 27 2007 - 16:53:21 CST

Perhaps we should mention the problem to the VMD developers too? Since, as
I said before, these are mol2 files generated from a normal-looking molecule
in VMD.

David

On 3/27/07, Scott Brozell <sbrozell_at_scripps.edu> wrote:
>
> 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_at_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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