VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Dec 08 2021 - 07:30:05 CST

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
says
auto none
within the segment statement, e.g. one line before
pdb "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 psfgen
> topology ct800342w_si_002.txt
> segment IS{
> first NTER
> last CTER
> pdb "cluster.pdb"
> }
> coordpdb cluster.pdb IS
> guesscoord
> writepdb IS.pdb
> writepsf 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 Peter
> Yes, 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!tUDoSBAto1tRDwoXGdLFd9Qh8-zLRb0wNOhgGe6kMnUzz6jwqDRSMBmn6jeKDHQt6w$
> <https://urldefense.com/v3/__https://pubs.acs.org/doi/abs/10.1021/ct800342w__;!!DZ3fjg!v7RiMBjlKWvvElEAMeJzxTDEExBYx-xwV89Hfs1X80WZPuBeKxE7NBGPdPALwSKLRQ$>".
> (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
>
>