On Mon, Aug 26, 2002, amber_at_heimdal.compchem.ucsf.edu wrote:
>
> I have noticed a problem when specifying the leaprc file.
> If I want to load the leaprc.rna.ff99 it does not map the residues
> according to the addPdbAtomMap command. Although all the names are
> mapped with the command leap (from AMBER7) does not map them. Meanwhile
> the leap of AMBER6 maps the residues if I specify the same addPdbAtomMap
> command in the leaprc file.
> Does anyone have any ideea what might happen here?
Can you provide more specific information? Are some residues mapped and not
others? What is in the pdb file itself for the residue name? And what does
it become inside leap (I assume you are using loadPdb?)
Try the dna version (leaprc.ff99): does that map things do DNA with your
input files? A little bit of sleuthing may help to narrow down the problem.
My best guess from the above is that the residue in your pdb file don't match
anything that leap expects to know about, so be sure to give an (small)
example file that fails to work....
..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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Received on Mon Aug 26 2002 - 18:09:22 PDT
