Hi,
When loading a PDB file, xleap will automatically add hydrogens to
residues that it recognizes based on the currently loaded parameters.
For example, if you have loaded the FF99SB forcefield (source
leaprc.ff99SB) and then load your PDB file (m = loadpdb test.pdb) any
residues defined in the 99SB parameter set (ALA, ASP, etc) will have
hydrogens added. You can see the currently loaded parameters with the
'list' command.
-Dan
On Mon, Jan 23, 2012 at 7:43 AM, <abinayar.imsc.res.in> wrote:
>
>
>
> Dear amber users,
>
> How exactly do I add Hydrogens to my protein crystal pdb
> structure? Does xleap automatically add Hydrogens to the protein
> structure once I load the structure through xleap program?
>
> Regards,
> Abinaya
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Mon Jan 23 2012 - 06:30:04 PST
