AMBER Archive (2008)

Subject: Re: AMBER: problems with sleap

From: Alan (alanwilter_at_gmail.com)
Date: Thu Jun 05 2008 - 01:48:03 CDT

Sorry, later I noticed I was not being clear. I guess it because I so
annoyed with 'basic_string::substr' that I didn't pay attention the rest.
But here goes in attach 2 pdbs.

dmp.pdb (from pdb 1BVG)

AAA.pdb (created with pymol)

mol2 files can be generated with babel.

I also noticed that sleap might not like sybyl atom definitions, only
gaff/amber atom types, is that right?

Many thanks advance.

Cheers,
Alan

On Thu, Jun 5, 2008 at 12:52 AM, David A. Case <case_at_scripps.edu> wrote:

> On Wed, Jun 04, 2008, Alan wrote:
> >
> > sleap -f sleap.in >| sleap.out
> >
> > For one I got top and xyz, but all others, I got this:
> > [snip]
> > [gtkleap]$ X = loadpdb mypdb.pdb
> > basic_string::substr
> >
> > and it failed.
> >
> > What's wrong with my pdbs?
>
> Without seing your files, it's hard to be of much help. There may be
> nothing
> wrong with the pdb files -- the fastbld part of sleap is very new, and
> might
> not work for all molecules. Can you post an example that gives the
> above error?
>
> ...dac
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-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
  • chemical/x-pdb attachment: AAA.pdb
  • chemical/x-pdb attachment: dmp.pdb
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