[Chimera-users] chimera minimize script

Bylund, Tatsiana (NIH/NIAID) [F] tatsiana.bylund at nih.gov
Mon Aug 8 19:22:01 PDT 2016

Thank you, Eric!

Do you know how do I save minimized file in a pdb format?

I tried

rc("minimize spec ':1-97.C z<10.0 & :.G|:1-97.C z<10.0 & :.F|:1-97.C' nsteps 100 cgsteps 0")
rc("write 'newfile.pdb'")

It does the minimization, but doesn't write the file

MidasError: "'newfile.pdb'" is not a model number

Error while processing chimera_mini.py:"

Thank you!

From: Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>>
Reply-To: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> BB" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Date: Monday, August 8, 2016 at 2:33 PM
To: "Bylund , Tatsiana (NIH/NIAID) [F]" <tatsiana.bylund at nih.gov<mailto:tatsiana.bylund at nih.gov>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] chimera minimize script

Hi Tatsiana,
Residue 33 in chain K (an ASN) in your structure is missing the side chain.  Since the first thing you do in your script is add hydrogens, Chimera adds two hydrogens to the carbon alpha of that residue.  Since those hydrogens have no corresponding molecular mechanics parameters in the Amber database, the minimization didn’t work.
You should not addh/addcharge in your script and instead run DockPrep.  See this dock-fans posting for how to do that:   [Dock-fans] dock prep in batch mode?<http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html>  That posting talks about adding keyword arguments you want to the prep() call.  If you want to use Gasteiger charges, add “method=‘gasteiger’” to the call.


Eric Pettersen
UCSF Computer Graphics Lab

On Aug 8, 2016, at 10:06 AM, Bylund, Tatsiana (NIH/NIAID) [F] <tatsiana.bylund at nih.gov<mailto:tatsiana.bylund at nih.gov>> wrote:

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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