VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat Mar 16 2019 - 18:34:51 CDT

John,

  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

Biophysics

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

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/