[Chimera-users] chimera minimize script

Bylund, Tatsiana (NIH/NIAID) [F] tatsiana.bylund at nih.gov
Mon Aug 8 10:06:11 PDT 2016

Dear all,

I need to minimize a lot of protein complexes and am trying to do it with a script.
I have a protein complex structure without Hydrogens, but when they are added in Chimera, it outputs error

Non-standard atom names:

ASN HA2 (:33.K at HA2)

ASN HA3 (:33.K at HA3)

Total charge for #0: 32.039

Total charge for #0: 32.039

The following residues had non-integral charges:

:33.K 0.039

Correct charges are unknown for 2 non-standard atom names in otherwise standard residues

Charges of 0.0 were assigned to the unknown atoms

1 model(s) had non-integral total charge

Details in reply log

Dock prep finished

Error while processing chimera_mini.py:

No MMTK name for atom "HA3" in standard residue "ASN"

When I delete residue K 33 (which DOES NOT have H in pub file) chimera runs minimization.

Would you have any suggestions?

Thank you!

Kind regards,
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