AMBER Archive (2007)

Subject: AMBER: amber with periodic condition

From: Mattia Mori - CERM (mori_at_cerm.unifi.it)
Date: Mon Oct 29 2007 - 11:16:14 CST

Dear amber users,
I'm trying to apply sander for a molecular dynamics steps of a solvated peptide after some minimizations steps.
In tleap I've loaded the pdb of the minimized peptide including the waterbox used during minimization, but when I try to impose ntb=2 I always get this error:  

Flags:
getting new box info from bottom of inpcrd
peek_ewald_inpcrd: Box info not found in inpcrd
Largest sphere to fix in unit cell has radius = 0.000

how can I work in periodic conditions starting from a water-including pdb? How can I impose my box dimension?
thank you

Mattia Mori


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