AMBER Archive (2007)

Subject: Re: AMBER: Fwd: [chirality.c] Atom did not match

From: David A. Case (case_at_scripps.edu)
Date: Fri Nov 16 2007 - 18:03:33 CST

On Fri, Nov 16, 2007, Francesco Pietra wrote:

> I further checked that step (4) below does not give problems when loading a
> single POPC molecule:
>
> model = loadpdb "popc.pdb"
>
> edit model
>
> May it be that problems to leap (and not to either VMD or Chimera) arise from
> how membrane.pdb is written, i.e. without TER records separating the various
> molecules?

Not having TER cards in the proper place will certainly lead to bad things
inside leap, and "chirality" problems are likely to one of them, since LEaP is
likley to try to create bonds between chains if TER cards are not present.

...dac

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