Maybe you used Accelrys for converting to pdb. Troubles concern only Amber
specific residues HIE and CYX (disulfide bond forming CYS). Also ptraj does
not write CONECT lines.
****
REMARK Accelrys Discovery Studio PDB file
REMARK Created: Mon Jan 04 11:15:38 Romance Standard Time 2010
****
Sincerely,
Dmitry Mukha
2010/1/12 Andrew Voronkov <drugdesign.yandex.ru>
> Dear amber users,
> by some reasons after clustering of mdrcd trajectory I get protein files
> with HETATM records for some amino acids (attached below).
> If I convert resulted rst file from mdcrd then everythinbg is ok.
> What can be the problem? (it's not difficult to replace them of course, but
> it s just strange a bit).
>
> Sincerely yours,
> Andrey
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Received on Tue Jan 12 2010 - 10:00:02 PST
