VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Fri May 04 2018 - 17:09:55 CDT

Dear Stuart,

to comment on the way to fix the issue that you are facing, I would need to
know more details about your system. The patches that you defined in QwikMD
are applied before the "regenerate angles dihedrals" command.

If you are certain the angle should not be declared and QwikMD is
introducing that error, QwikMD might not be the right tool for your system,
and I should figure a way to incorporate patches after the regenerate
command. One fix that you may try is to delete the declaration of that
specific angle in your psf file generated by QwikMD.

Best

On Thu, May 3, 2018 at 11:53 AM Rose, Stuart Wallace <swrose_at_illinois.edu>
wrote:

> Hello,
>
> My model includes a hetero "residue" which is patched in via two liganding
> histidines. The namd session times out and the log tells me there is a
> angle parameter missing. This angle parameter does not exist (the angle is
> the N - Fe - N which probably should not have angle parameter). The psfgen
> autogenerate command may be generating this angle. The comments on the
> patch specify that the patch should be applied after autogenerate.
>
> What is the best way to approach this? Should I give up on QwikMD for
> this model? or is there a way to fix this?
>
> Thank you in advance.
>
> Stuart
>
>
> *********************************************************************************
> Stuart W. Rose, PhD
> E-Mail: swrose_at_illinois.edu
> University of Illinois @ Urbana-Champaign Office: 153
> Davenport Hall
>
> 607 S. Mathews Avenue
> Urbana, IL 61801
>
>
> Lab Ph. (217)333-7407
> Center for Biophysics & Quantitative Biology Office: Loomis,
> MC-704
>
> *********************************************************************************
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851