Jake Isaacs wrote:
>
> When I use InsightII to view a pdb file created from prmtop
> and inpcrd via ambpdb, multiple anomalous bonds appear.
> What might be the cause and solution for this?
>
Assuming that your pdb is for a protein or a DNA (i.e. with
standard residues InsightII recognizes), are there only heavy
atoms or did you include hydrogens also? My experience is that
since there are no unique labelling for the H's (e.g. a 3HA in
AMBER might be a 2HA in InsightII), many of the AMBER H's will
be unknown atoms to InsightII ... thus the anomalous bonds.
Hope it helps,
Elsa
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«L'amore che muove il sol e l 'altre stelle»
Dante Alighieri
(La Divina Commedia)
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Elsa F. Sousa Henriques e-mail: eshenriq_at_fc.up.pt
Dept. Quimica, FCUP phone: +351-22-6082827
Rua do Campo Alegre, 687 fax: +351-22-6082959
4169-007 PORTO
Received on Mon Apr 16 2001 - 10:49:03 PDT
