On Wed, Aug 11, 2010, Karan Mehra wrote:
> These are the exact commands that I ran with sleap:
>
> $sleap
> [gtkleap]$ source /itc/common/amber/10/amber10/dat/leap/cmd/leaprc.ff99SB
> [gtkleap]$ set default fastbld on
> [gtkleap]$ ctx = loadpdb ctx.pdb
> Warning: there is more than one bond made between two neighbouring residues,
> maybe cutoff is too small?
> Warning: there is more than one bond made between two neighbouring residues,
> maybe cutoff is too small?
> Warning: there is more than one bond made between two neighbouring residues,
> maybe cutoff is too small?
I don't get these warnings. First step would be to upgrade to the current
version of AmberTools to see if the problem goes away.
(Potentially) faster workarounds: (1) leave out the fastbld command--this
is not needed anyway for a simple protein; (2) use tleap instead of sleap.
...good luck...dac
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Received on Wed Aug 11 2010 - 13:00:06 PDT
