Yes, I've found it couple minutes after sending this email:)
You are absolutely right. Sorry for the disturbance. Everything is ok with PTRAJ in this case.
Best regards,
Andrew
12.01.10, 19:44, "Dmitry Mukha" <dvmukha.gmail.com>:
> 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
>
> > 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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> >
> >
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Received on Thu Jan 14 2010 - 01:30:03 PST
