VMD-L Mailing List

From: Kiana Jahani (kiana.jahani_at_REMOVE_yahoo.com)
Date: Mon Dec 06 2021 - 02:19:29 CST

 Dear Peter,
Thank you so much for your reply. I used the topology and parameter files from the supporting information of the related reference "https://urldefense.com/v3/__https://pubs.acs.org/doi/abs/10.1021/ct800342w__;!!DZ3fjg!vicRH_oqJo2jHZSinTC5wdzUN3HNqQin_qEUFp4ebRJ3Jr5BwBWfuPuK8JiwIfMqiQ$ ". (ct800342w_si_002.txt and ct800342w_si_003.txt files).The previous error was for F4O cluster. Actually I got the same error for F4R and FHO clusters.
Best,Kiana

    On Sunday, December 5, 2021, 08:43:36 PM GMT+3:30, Peter Freddolino <petefred_at_umich.edu> wrote:
 
 What parameter files are you including, and what topology files did you use in building the iron sulfur cluster? Most likely you don't have the parameter file included that would contain the parameters for this cluster.Best, Peter

On Sun, Dec 5, 2021 at 8:25 AM Kiana Jahani <kiana.jahani_at_remove_yahoo.com> wrote:

Dear VMD Users
I generated the psf file from a pdb file using psfgen. For minimization, I got the following error:FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR FEJO SJO FEJO SJO (ATOMS 75913 75919 75915 75918)The atoms refer to iron sulfur cluster present in protein.I also added "auto angles dihedrals" to the psfgen script but the result didn't change.
I would appreciate it if anyone can help me with that. If more information is required, please just let me know.
Best,
Kiana