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@HA2) ASN HA3 (:33.K@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
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 Eric Pettersen UCSF Computer Graphics Lab
On Aug 8, 2016, at 10:06 AM, Bylund, Tatsiana (NIH/NIAID) [F] <tatsiana.bylund@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@HA2)
ASN HA3 (:33.K@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 <chimera_mini.py>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Reply-To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Date: Monday, August 8, 2016 at 2:33 PM To: "Bylund , Tatsiana (NIH/NIAID) [F]" <tatsiana.bylund@nih.gov<mailto:tatsiana.bylund@nih.gov>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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 Eric Pettersen UCSF Computer Graphics Lab On Aug 8, 2016, at 10:06 AM, Bylund, Tatsiana (NIH/NIAID) [F] <tatsiana.bylund@nih.gov<mailto:tatsiana.bylund@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@HA2) ASN HA3 (:33.K@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 <chimera_mini.py>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tatsiana, As the error message suggests, your write command is incorrect and needs a model-number argument, e.g. write #0 newfile.pdb There are other options that might also be useful: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 8, 2016, at 7:22 PM, Bylund, Tatsiana (NIH/NIAID) [F] <tatsiana.bylund@nih.gov> wrote:
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!
participants (3)
-
Bylund, Tatsiana (NIH/NIAID) [F] -
Elaine Meng -
Eric Pettersen