Do you have templates for residues in these compounds? If so, you can
just loadpdb and savepdb in a leap script.
If no templates, and you just want Amber to add H's where chemically
appropriate, it might be possible to adapt xleap's 'Add H' utility to
something scriptable - e.g. try this in xleap:
> x = loadpdb my_h_less.pdb
> bondbydistance x
> edit x
then select all atoms and try the Add H and Build option (written by
Chris Schafmeister). The tricky part is determining the elements from
the atom names at load time - this must be reliable. A loadPdbAsNewRes
command could wrap all this into one graphics-free step.
But likely as not there is a more available solution in some other program.
Bill
On 4/18/17 1:57 AM, jacob wick wrote:
> Dear all,
>
> I have a library of compounds which do not have explicitly added Hydrogens.
> The data is in .sdf or .pdb file formats.
> Can some amber module be used to do this? If so, please guide.
>
> Jac
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Received on Tue Apr 18 2017 - 02:30:03 PDT
