Hi,
> Created a new atom named: H within residue: .R<NGLY 7>
[...]
> The file contained 111 atoms not in residue templates
All these errors are for hydrogen atoms. Likely, your pdb contains Hs that
do not conform to Amber naming expectations, which confuses leap. Maybe
removing all hydrogens from the pdb and having leap re-add them is the
easier way to go.
> In my opinion, before loadpdb step, I should do some changes in
[...]
> all_amino03.in file. Then I did changes in pdb file so that after loadpdb
It very much depends on what those changes were to judge if the next is a
real problem or just a visualization issue. I would suggest trying just
without the hydrogens and see what leap then tells you.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Jan 31 2012 - 07:30:03 PST
