AMBER Archive (2005)

Subject: Re: AMBER: question about loadiing pdb file of a molecule complex

From: David A. Case (case_at_scripps.edu)
Date: Tue May 31 2005 - 13:00:59 CDT

On Mon, May 30, 2005, gtg549i_at_mail.gatech.edu wrote:

> Attachment are the files of pdb. mol1.pdb is the first molecule, mol2.pdb is
> the second molecule, complex.pdb is the initial structure of complex of
> molecule1 and molecule2.

> > > 4.When i try to load it into xleap, the following messages come out:
> > > !FATAL ERROR----------------------------------------
> > > !FATAL: In file [chirality.c], line 142
> > > !FATAL: Message: Atom named C1 from MAA did not match !
> > > !
> > > !ABORTING.

I can't see any problems, using loadpdb to load complex.pdb into LEaP. Can
you give the *exact* sequence of commands that you gave to encounter this
error?

Note that you have _very_ short distances between the two molecules: O5 of MAA
and C10 of BE2 are only 1.6 Ang. apart. O5 of MAA and H74 of BE2 are only
1.3 Ang. apart. This should still not cause problems because you have a TER
card between the systems, but you might see if the problem is related to
having such a bad starting geometry.

...dac

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