DSSP wont run for one chain of dimeric peptide connected by dissulfide bond

User discussions
1

GROMACS version: 2022
GROMACS modification: No

I’m trying to run gmx do_dssp on a dimeric peptide in which the chains are connected by a dissulfide bond. When generating the topology with pdb2gmx I merged both chains into a single molecule.

But when I try to run gmx do_dssp it simply goes into an infinity loop and never stops. So I tried indexing each chain separately. It worked for one chain but not for the other.

I know it probably has something to do with the dissulfide bond, but it doesn’t make any sense.

Odly enough gmx dssp from Gromacs 2023, works for it, but it won’t generate the dssp plot that really I need.

I’m 100% certain that my dssp is setup correctly, it works for literally everything else. I’ve checked multiple times.

Thanks

2

Does gmx dssp in GROMACS 2024 work for you? Otherwise, what plot types are you missing?

4

Hi, Thank you for your reply.

I’m missing the following plot type:

image

I really need this plot because it’s how we have always performed secondary structure analysis in our group. It seems gmx dssp is incapable of producing such a plot.

5

Does this thread (not the first posts) help How to read the dssp.dat file gmx 2023.1?

6

Hi, thank you for your reply, unfortunately this thread doesn’t help me. I really need the dssp graph in which the secondary structures are represented by colors and we have the residue numbers on the y axis (like I previously showed). It is generated as a xpm file which you can convert to a eps file using gmx xpm2ps.

I really need to find a work around to make gmx do_dssp work for both chains.

I know it might be a problem only I have, but I really need the old gmx do_dssp functionality. I’d really appreciate if it was added to gmx dssp in the future.

7

I understand. Could you, please, submit a new feature request issue at Issues · GROMACS / GROMACS · GitLab?

8

Sure, thanks