On Sat, Jan 23, 2016, ankita mehta wrote:
> When I m creating the prmtop and inpcrd of a pdb file , I get following
> statements :
> Created a new atom named: HD2 within residue: .R<ASP 9>
> Created a new atom named: HE2 within residue: .R<GLU 18>
> Created a new atom named: HE2 within residue: .R<GLU 41>
> Created a new atom named: HE2 within residue: .R<GLU 51>
> Created a new atom named: HE2 within residue: .R<GLU 52>
> Created a new atom named: HD2 within residue: .R<ASP 54>
> Created a new atom named: HE2 within residue: .R<GLU 66>
> Created a new atom named: HE2 within residue: .R<GLU 73>
It looks like your pdb file contains protonated carboxylates; but the residue
names do not reflect this. You need to edit the pdb file to change the
residue names for the residues listed above to ASH or GLH (which is Amber's
choice for the protonated forms.)
[Jason, other developers: does pdb4amber recognize these the way it examines
hydrogen atoms in histidines to get the correct residue name? It not, that
should be added....]
> Added missing heavy atom: .R<CARG 78>.A<OXT 25>
This is OK, assuming that ARG 78 is indeed supposed to be a C-terminal
residue.
...dac
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Received on Sat Jan 23 2016 - 13:00:02 PST
