VMD-L Mailing List

From: Kiana Jahani (kiana.jahani_at_REMOVE_yahoo.com)
Date: Thu Dec 09 2021 - 02:37:41 CST

 Dear Peter
You are right, I got it. I used the command
segment IS {pdb cluster.pdb}for building the segment of the cluster specifically, but it also contains auto dihedrals. I should use the command that you said.
Thank you so much for your help and time. I really appreciate it.
Best,Kiana

    On Wednesday, December 8, 2021, 06:46:34 PM GMT+3:30, Peter Freddolino <petefred_at_umich.edu> wrote:
 
 Hi Kiana,If you're making an iron-sulfur cluster (not a protein), you should have NONE as your N and C terminal patches instead of NTER/CTER (which are specific to proteins). Also, per my last email, you should add a line that saysauto nonewithin the segment statement, e.g. one line beforepdb "cluster.pdb"
Best,Peter

On Wed, Dec 8, 2021 at 1:34 AM Kiana Jahani <kiana.jahani_at_yahoo.com> wrote:

 Dear Peter
You are right. I made a mistake with the other cluster not F4O in the topology file. The script that I used for building psf is:
package require psfgentopology ct800342w_si_002.txtsegment IS{first NTERlast CTERpdb "cluster.pdb"}coordpdb cluster.pdb ISguesscoord
writepdb IS.pdbwritepsf IS.psf
Best,
Kiana
    On Tuesday, December 7, 2021, 06:43:25 PM GMT+3:30, Peter Freddolino <petefred_at_umich.edu> wrote:
 
 Hi Kiana,Where in the topology file is that dihedral showing up? Perhaps I missed it but I didn't see any definition of it. How are you building your psf? Can you post your script? You might need to explicitly add "auto none" to the segment block for the iron-sulfur cluster.Best,Peter

On Tue, Dec 7, 2021 at 6:30 AM Kiana Jahani <kiana.jahani_at_yahoo.com> wrote:

 Dear PeterYes, the error is "unable to find dihedral parameters for FEJO SJO FEJO SJO". I think you mean by using the term "auto angles dihedrals" in the script, all possible dihedrals will be generated. Actually I tried both, with and without this term, but the result didn't change. The topology file defines this dihedral but it isn't contained in the parameter file. Do you think the problem can not be solved (by this parameter file)?
Best,
Kiana

    On Monday, December 6, 2021, 05:27:19 PM GMT+3:30, Peter Freddolino <petefred_at_umich.edu> wrote:
 
 Dear Kiana,Are you sure that there is supposed to be a 'FEJO-SJO-FEJO-SJO' dihedral term? It does not appear in the parameter file, and it looks like the topology likewise does not define Fe-S-Fe-S dihedrals, so I suspect that you want to AVOID using automatic dihedral generation for this chain. Using AUTO DIHE will generate all possible dihedrals for atoms with the appropriate bonding pattern, but it looks like such dihedrals are not intended in this force field for the iron-sulfur cluster.
Best,
Peter

On Mon, Dec 6, 2021 at 3:20 AM Kiana Jahani <kiana.jahani_at_yahoo.com> wrote:

 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!qCl-qZRz1ztHG7pp9UQ2Vl2K669gpjaUO9uccS6iHAvZ3W1EGWTwu5WdPqucERs48g$ ". (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