On Tue, May 11, 2010, RINU KHATTRI wrote:
>
> hello sir iam a student doing work on simulation on rnase using amber8
> tool i hav eproblem in tleap program the out put given several error
> during bond connect my input file is file obtained from modeller 9v7 tool
> its an 1fs3 pdb id in which one peptide is removed an modelled the
> structure the error are
These are not errors: they are informational messages. Presumably your
input structure has a -6 charge (is that correct) and some close distances
(you can also check these). The bad contacts will probably go away if you
do some initial minimizations.
> WARNING: The unperturbed charge of the unit:
> 6.000000 is not zero.
> Warning: Close contact of 1.655710 angstroms
> between .R<THR 3>.A<HG23 10> and .R<ALA 5>.A<H 2>
.etc.
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 11 2010 - 07:30:04 PDT
