[Chimera-users] chimera minimize script

[Bylund, Tatsiana (NIH/NIAID) [F]]

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,
Tatsiana
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