AMBER Archive (2003)

Subject: Re: AMBER: problem in tleap

From: aini_at_UMDNJ.EDU
Date: Fri Oct 24 2003 - 14:23:33 CDT

Thanks for dac's suggestions!
I deleted the three atoms and then tleap stopped complaining about the end
phosphate group. However the fatal error is still there. And I checked my pdb
file and believe there is not extra atom. What else may give this fatal message?

aini

Quoting "David A. Case" <case_at_scripps.edu>:

> On Fri, Oct 17, 2003, aini_at_UMDNJ.EDU wrote:
> >
> > I am trying to run a MD simulation on a protein-DNA-ligand complex. I
> wrote a
> > script to run tleap automatically to generate input files. I got an error
> > message:
> >
> > Loading PDB file: ./new5mht.pdb
> > Created a new atom named: P within residue: .R<DC5 329>
> > Created a new atom named: O2P within residue: .R<DC5 329>
> > Created a new atom named: O1P within residue: .R<DC5 329>
>
> Your pdb file apparently has a phosphate at the 5' end of one of the
> chains(?). This is not the default behavior the LEaP assumes (which is a 5'
> OH group). If you really need the phosphate group, you will have to define
> your own residue. There is an example of this in the tRNA files at
> http://pharmacy.man.ac.uk/amber/ that might help.
>
> > !FATAL ERROR----------------------------------------
> > !FATAL: In file [chirality.c], line 115
> > !FATAL: Message: No C5 in aaOrig list
> > !
> > !ABORTING.
> >
> > The "DC5 329" is the 5'-Cytosine in one DNA strain. I found "chirality.c"
> file
> > but I don't know what the aaOrig list means.
> >
>
> I'm not sure about this one, but it plausibly is related to the extra atoms
> in
> your pdb file. Can you remove the three atoms listed above, and see what
> happens?
>
> ..dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
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