VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Mar 16 2019 - 01:13:06 CDT

Kelly,
  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
  vmd_at_ks.uiuc.edu

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 NormalSCF
> 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 load
> any orbitals. I also tried using orcaviewer.tcl to open the orca viewer
> plugin, but no orbitals are loaded. This is what VMD's console reads:
> 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 I
> don't use it, my QMMM minimization takes 305 hours. With the SCF block,
> 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
http://www.ks.uiuc.edu/Research/vmd/