[gmx-users] including missing atoms

[ran at hemi.tau.ac.il]

Dear Alan,

You can use profix, from Prof. Barry Honig's lab
http://honiglab.cpmc.columbia.edu/

Ran.

Quoting Alan Wilter Sousa da Silva <alan at lncc.br>:

>
> Hi List!
>
> I know that GMX warns about missing atoms in PDB, and, if one wants, it'll
> generate an incomplete topology. However, is there no option of pdb2gmx to
> rebuild automagically the missing atoms to complete such deficient residue
> and have a complete topology (but, of course, warned about that)? If I'm
> not wrong, spdbviewer can do that.
>
> If GMX is able to do that, can someone suggest another programme which
> would be able to achieve that automaticaly?
>
> Thanks in advance for any help.
>
> Cheers,
> Alan
>
> --
> --------------------------
> Alan Wilter Sousa da Silva
> --------------------------
> D.Sc. - IBCCF/UFRJ
> Projeto BioPAUA - HP/LNCC
> Petrףpolis (RJ), Brasil
> www.lncc.br/~alan
>
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