On Fri, Feb 14, 2014, Jorgen Simonsen wrote:
>
> I am trying to make restraints to zinc ions in a protein I would like to
> run a MD simulatoin on but I get the following error :
>
> # makeDIST_RST
> Currently configured for up to 50000 atoms
> Using MAP file ~/amber12/dat/map.DG-AMBER
> ERROR no map function for ZN ZN :data= 333 ZN ZN 23 HID
> NE2 2.1
>
> I ran the cmd
>
> ~amber12/bin/makeDIST_RST -upb rst_file -pdb tmp.pdb -rst RST.dist
>
> the 7-column file looks like this
>
> 333 ZN ZN 23 HID NE2 2.1
>
The default in makeDIST_RST is to not map an atom to itself; the original
intent was for NMR data, to be very conservative and treat unknown
atom/residue entries as an error. That can be an effective filter against
typos in input restraint files (which might be rather large files).
So, you just have to edit ~/amber12/dat/map.DG-AMBER, and add a ZN residue
entry, and have it map ZN to ZN. Once you look at the file, the format will
be obvious.
(We probably should add some command-line option to map atoms to themselves if
they are not otherwise mapped. It's actually on my to-do list, or perhaps more
realistically, my "to-not-do" list....)
...dac
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Received on Fri Feb 14 2014 - 13:00:02 PST
