On Tue, Feb 02, 2016, Sivanandam M wrote:
>
> WARNING: The unperturbed charge of the unit: -9.000000 is not zero.
> FATAL: Atom .R<GLU 202>.A<HE2 16> does not have a type.
> FATAL: Atom .R<HIE 253>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 284>.A<HD1 18> does not have a type.
> FATAL: Atom .R<GLU 285>.A<HE2 16> does not have a type.
> FATAL: Atom .R<HIE 322>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 387>.A<HD1 18> does not have a type.
> FATAL: Atom .R<ASP 400>.A<HD2 13> does not have a type.
> FATAL: Atom .R<HIE 405>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 447>.A<HD1 18> does not have a type.
> FATAL: Atom .R<ASP 494>.A<HD2 13> does not have a type.
> FATAL: Atom .R<CALA 542>.A<HXT 12> does not have a type.
The problem is with the hydrogens. Using pdb4amber will fix the histidine
problems, but your input pdb file (from where?) has protonated carboxylates,
including a protonated c-terminal residue.
If you really want protonated carboxylate side chains, you need to manually
edit the PDB file to change GLU to GLH, and ASP to ASH.
Amber does not currently offer much support for protonated c-terminal
residues. You will have to learn to make a custom residue there if you really
need that to be protonated.
If you don't care, and/or want fairly standard protonation states (apprpriate
for neutral pH), then the earlier advice is fine: remove the hydrogens from
the pdb file (say using "pdb4amber --nohyd"), and let LEaP rebuild them.
....dac
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Received on Tue Feb 02 2016 - 05:00:04 PST
