AMBER Archive (2008)

Subject: Re: AMBER: problems with sleap

From: Alan (alanwilter_at_gmail.com)
Date: Mon Jun 16 2008 - 11:07:24 CDT

Thanks David, pretty good know this. So far I am doing well with tleap.
Many thanks again.

Alan

On Mon, Jun 16, 2008 at 4:48 PM, David A. Case <case_at_scripps.edu> wrote:

> On Thu, Jun 05, 2008, Alan wrote:
>
> > 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?
>
> To make a prmtop, you need gaff or amber atom types, for sure.
>
> We think we have the problem fixed (i.e. you can set fastbld to "on", and
> load
> and save dmp.pdb), with no "substr" messages. The fix will be incorporated
> into version 1.1 of AmberTools, which will be announced soon. [There have
> been lots of changes to sleap since version 1.0, so trying to provide
> individual patches seems likely to cause more harm than good.]
>
> Thanks again for reporting this...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<<

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