AMBER Archive (2007)

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

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Nov 16 2007 - 15:59:40 CST

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?

f.

--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> Date: Fri, 16 Nov 2007 09:09:10 -0800 (PST)
> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: [chirality.c] Atom did not match
> To: Amber <amber_at_scripps.edu>
>
> I am trying to use a POPC bilayer in Amber9. What I did:
>
> (1) Created a 100x100A (smaller is not enough for my protein) POCP
> membrane.pdb
> file with membrane plugin in VMD.
>
> (2) Took a single POPC and successfully got prepin file with
> Antechamber/divcon
> (which found no problems, as revealed by running parmchk).
>
> (3) Using leaprc.ff99SB and gaff in xleap, loaded prepin. POPC seemingly OK
> from "check POP" "edit POP".
>
> (4) Command
>
> model = loadpdb "membrane.pdb"
>
> reported
>
> FATAL ERROR
> FATAL: In file [chirality.c], line 142
> FATAL: message: Atom named C217 from POP did not match!
> ABORTING
> ____________
> Hope not to have overlooked any precise answer from searching through the
> mailing list archives. I do not understand the "chirality" because C217 is at
> the penultimate methylene group of the longest fatty chain, so that no
> chirality. Unless the wish of loading that way all the POPC molecules was
> wrongly based .....
>
> Thanks
> francesco pietra
>
>
>
>
>
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