On Tue, May 22, 2018, Timothy Cholko wrote:
>
> Here's GLD.lib and the pdb:
> --------------------------------------------------------------------
> !!index array str
> "GLD"
> !entry.GLD.unit.atoms table str name str type int typex int resx int
> flags int seq int elmnt dbl chg
> "AU" "AU" 0 1 131075 1 79 0.0
> "AU" "AU" 0 2 131075 1 79 0.0
> "AU" "AU" 0 3 131075 1 79 0.0
> "AU" "AU" 0 4 131075 1 79 0.0
Atom names within a residue (like "GLD" have to be unique). We check
for this in PDB files, but somehow this didn't get checked in the way
you created your .lib file.
>
> ATOM 1 AU GLD 1 0.000 0.000 0.000 1.00 0.00
> ATOM 2 AU GLD 2 0.000 2.039 2.039 1.00 0.00
> ATOM 3 AU GLD 3 2.039 0.000 2.039 1.00 0.00
> ATOM 4 AU GLD 4 2.039 2.039 0.000 1.00 0.00
There is a fundamental disconnect here: your GLD library has four gold
atoms, but your pdb file has just 1 gold atom in each residue. The pdb
file looks fine, but you should change your library to have just a
single gold atom inside the GLD residue.
>
> A couple other things: can you run MD on atoms of an unknown element as far
> as Leap is concerned, i.e. a "?" in the "element" column of the edit atoms
> table in Xleap
No: you need to have an addAtomTypes command in your leap script to
define the type of atom. (Some aspects of MD can get along without
this, but it's better to have such an entry--look at the leaprc files
in $AMBERHOME/dat/leap/cmd for examples.)
....dac
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Received on Tue May 22 2018 - 18:00:03 PDT
