From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Tue Mar 19 2019 - 12:31:43 CDT
I just installed the latest VMD, a31, and the orbital loading problem appears to have been fixed. In this version, I can now load all of my orbitals.
Kelly L. McGuire
Department of Physiology and Developmental Biology
Brigham Young University
Provo, UT 84602
From: John Stone <johns_at_ks.uiuc.edu>
Sent: Sunday, March 17, 2019 6:19 PM
To: McGuire, Kelly
Cc: VMD Mailing LIst; namd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: ORCA Orbital Bug
Indeed, the mailing lists will silently block large file attachments
from being posted, however I received what you sent since you included
my email address in the To: line directly. I will have a look at this
when I get back from the GPU conference in about a week. I'm sure you're
right about the difference in behavior between the alpha12 and
alpha27 versions of VMD, we're in the process of rewriting the code
to make it more portable and we undoubtably broke something in the newer
rev that now needs to be corrected.
On Sat, Mar 16, 2019 at 11:34:51PM +0000, McGuire, Kelly wrote:
> I responded to your email, but I attached a file. I'm not sure if
> emails with attachments get through to the NAMD forum.
> Kelly L. McGuire
> PhD Candidate
> Department of Physiology and Developmental Biology
> Brigham Young University
> LSB 3050
> Provo, UT 84602
> From: John Stone <johns_at_ks.uiuc.edu>
> Sent: Saturday, March 16, 2019 12:13 AM
> To: McGuire, Kelly
> Cc: VMD Mailing LIst; namd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: ORCA Orbital Bug
> This is undoubtably a limitation of the ORCA log parser.
> Can you provide us with example files the demonstrate both the
> working and non-working variants you've encountered?
> Best regards,
> John Stone
> On Fri, Mar 15, 2019 at 04:02:30PM +0000, McGuire, Kelly wrote:
> > Not sure if this is an NAMD or VMD bug. In my QMMM NAMD config file
> > (using ORCA), I have:
> > qmConfigLine "!RI BP86 def2-SVP def2/J Grid5 NoFinalGrid EnGrad
> > printbasis"
> > qmConfigLine "%%output PrintLevel Mini Print\[ P_Mulliken \] 1
> > Print\[P_AtCharges_M\] 1 end"
> > qmConfigLine "%%output Print\[ P_Basis \] 2 Print\[ P_MOs
> > \] 1 end"
> > qmConfigLine %%scf
> > qmConfigLine maxiter 500
> > qmConfigLine shift shift 0.1 erroff 0 end
> > qmConfigLine damp fac 0.80 erroff 0.001 end
> > qmConfigLine end
> > I use grab_orcah.sh to concatenate the Orca outputs into a .orc file.
> > When I try to open this in VMD and view the orbitals, VMD does not
> > any orbitals. I also tried using orcaviewer.tcl to open the orca
> > plugin, but no orbitals are loaded. This is what VMD's console
> > orcaplugin) Orca version: 4.0.1
> > Found commands.
> > orcaplugin) No molecule charge found. Exiting
> > orcaplugin) No molecule multiplicity found. Exiting
> > orcaplugin) Number of electrons not found. Exiting
> > New element found: H
> > New element found: C
> > New element found: N
> > New element found: O
> > New element found: Cu
> > New element found: H
> > orcaplugin) Parsed 975 uncontracted basis functions.
> > orcaplugin) Filled basis arrays.
> > orcaplugin) Found multiple appended gradient calculations: 12
> > orcaplugin) Timestep 0:
> > orcaplugin) ============
> > orcaplugin) Number of SCF iterations: 36
> > orcaplugin) Found wavefunction of type 0.
> > orcaplugin) ERROR. Only s/p/d/f-shells are supported.
> > orcaplugin) No canonical wavefunction present for timestep 0
> > orcaplugin) Frames read: 1
> > IF I remove the SCF block from my config file, then orbitals can be
> > loaded. BUT, I need those SCF commands to help with convergence. If
> > don't use it, my QMMM minimization takes 305 hours. With the SCF
> > it takes 90 hours.
> > Kelly L. McGuire
> > PhD Candidate
> > Biophysics
> > Department of Physiology and Developmental Biology
> > Brigham Young University
> > LSB 3050
> > Provo, UT 84602
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> Visible links
> 1. http://www.ks.uiuc.edu/~johns/
> 2. http://www.ks.uiuc.edu/Research/vmd/
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/
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