AMBER Archive (2003)

Subject: Re: AMBER: problem in tleap

From: David A. Case (case_at_scripps.edu)
Date: Fri Oct 17 2003 - 10:59:27 CDT

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 

-- 

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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:                   
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