AMBER Archive (2007)

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

From: Jojart Balazs (jojartb_at_pharm.u-szeged.hu)
Date: Fri Nov 16 2007 - 11:48:51 CST

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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