AMBER Archive (2007)

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

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Nov 16 2007 - 13:38:20 CST


Hi Balazs
Which file, please? I did everything for Amber9 on Debian Linux amd64 and for
VMD on Debian Linux i386, and there is no DOS on my machines.

I noticed your recent important paper on J Comp Chem. Next time I'll go
training my pointing breed on the Ukraine-Romania border may be I'll stop a
moment in Szeged to see you.

Thanks
francesco

--- Jojart Balazs <jojartb_at_pharm.u-szeged.hu> wrote:

> Dear Francesco,
> I obtained the same error massage, when i did not convert the file from
> dos to unix (dos2unix command).
> Hope this helps.
> Balazs
> Francesco Pietra wrote:
> > 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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