ADL: Mg's parameter

Eugenia Polverini eugenia.polverini at
Wed Feb 16 04:58:59 PST 2005

If you use the Python program (following the instructions at the
Autodock web page) you can obtain the file "new-parameters.txt" that
contains all the parameters you need for a lot of atoms and also Mg
(remember that what you obtain has to be multiplied by the coefficient
0.1485, see the user guide p.12).
In addition you have to set, in the pdbqs file, the Mg charge (2.0 for
the ion) and the atomic-fragmental-volume (in the next to last column)
that for Mg is 2.66.

Hoping this helps


ying xiong ha scritto:
> Dear autodock users:
>    I has Mg atom in my protein file. However ADT don't let me input its parameter because it has the first letter "M". It indeed has its parameter in *.gpf file(such as C-M, O-M).  Where are these parameters from ? Does it refer to Mg's parameter?
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ying xiong
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡yxiong at
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-02-15
> ________________________________________________
> --- ADL: AutoDock List  --- ---

Eugenia Polverini, Ph.D.
Dept. of Physics
University of Parma
Parco Area delle Scienze, 7/A
43100 Parma

Phone: +39 0521 905254
Fax: +39 0521 905223
E-Mail: eugenia.polverini at

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