[Chimera-users] Minimization and mystery nonstandard HIS atom name
pett at cgl.ucsf.edu
Thu Aug 22 16:06:43 PDT 2013
I think this is a problem that was fixed in May of last year, i.e. in versions 1.6.2 and later. What version are you using? If you are using 1.6.2+, please send me your structure file so I can track down the problem.
On Aug 22, 2013, at 2:35 PM, Jason L Burkhead <jlburkhead at uaa.alaska.edu> wrote:
> I am trying to minimize a protein structure and run into the following error:
> 'No MMTK name for atom "HND1" in standard residue "HIS"'
> My .pdb file specifies this atom as ND1, and if I change it to HND1 it still gives me the same error. Does anyone have any suggestions for a solution?
> The reply log is below:
> No incomplete side chains
> No SEQRES records for COMMD1_C_terminus_c.2.0.pdb (#0) chain A; guessing terminii instead
> Chain-initial residues that are actual N terminii: GLY 1.A
> Chain-initial residues that are not actual N terminii:
> Chain-final residues that are actual C terminii: ASN 73.A
> Chain-final residues that are not actual C terminii:
> 42 hydrogen bonds
> Hydrogens added
> Charge model: AMBER ff99SB
> Non-standard atom names:
> HIS HND1 (HIS 17.A HND1, HIS 22.A HND1)
> Total charge for #0: -4.000
> Correct charges are unknown for 1 non-standard atom names in otherwise standard residues
> Charges of 0.0 were assigned to the unknown atoms
> Details in reply log
> No MMTK name for atom "HND1" in standard residue "HIS"
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Chimera-users