AMBER Archive (2008)

Subject: Fwd: Re: AMBER: xleap screen output

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Mar 04 2008 - 11:33:34 CST

Perhaps I should mention that atom names related to GAFF are in capital letters
in the pdb files, like for leaprc.ff99SB. Though, they were so even for the
successful procedure with my former system
francesco

--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> Date: Tue, 4 Mar 2008 09:27:00 -0800 (PST)
> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: Re: AMBER: xleap screen output
> To: amber_at_scripps.edu
>
> I could reproduce the xleap preparation of prmtop/inpcrd files with the my
> previous membrane/protein/ligand system.
>
> Though this new system only differs in the ligand, it required a whole setup
> and I am still in open waters. I repeated the whole procedure (starting from
> the same best pose from DOCK) and the pdb layouts match those successful
> above.
>
>
> From the warning messages while creating models in xleap the problems seem to
> be with the membrane: xleap added 152 missing atoms. Curiously, it insists
> that, e.g. SH11 and RH11 do not have a type (atoms of the lipid), while in
> the
> pdb file these are correctly (correctly for leap) H11S and H11R. I.e., it
> says
> atom names are wrong, though they are right and correctly positioned in the
> file (13-16 columns) while single-letter atom names are at column 14. No
> warning message with the protein complex pdb.
>
> Probably the best would be to drop the matter for a week. until prejudices
> are
> over. At any event, as I could reproduce the former process, no bug in the
> program can be claimed.
>
> francesco
>
>
> --- Bill Ross <ross_at_cgl.ucsf.edu> wrote:
>
> > > FATAL: Atom .R<E 2700>.A<H 1> does not have a type.
> >
> > A residue name of 'E' sounds suspicious - if your residue names
> > don't include 'E' I would suspect the pdb file is malformed with
> > the residue name wrongly positioned. Since the error msg continues
> > with gibberish, it may be worthwhile for a developer to probe why
> > this is so, but in the short run you should double-check your pdb
> > format.
> >
> > Bill
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>
>
>
>
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