normal Accessing the DSSP binary

  • anjali
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10 years 4 months ago #3514 by anjali
Accessing the DSSP binary was created by anjali
Hi all,

I'm fairly new to Gromacs and UNIX scripting in general. I've been trying to use the martinize.py script to convert the 1UBQ.pdb file to a coarse-grained file.

Unfortunately, I get an error message whenever I try to access the DSSP binary (which also means that I'm losing secondary structure information).

My questions are:

1. Is there a specific location where I should store the dssp files? I usually store it in my home director (e.g, a4gopal/dssp) and my simulation files are stored in another folder (e.g., a4gopal/protein)
2. The code I use to call the dssp is as follows:
./martinize.py -f 1UBQ.pdb -o system.top -x cg_1UBQ.pdb
                 -dssp ../dssp/ -p backbone -ff martini22

I've tried variations of this and it doesn't work.

Any help/suggestions on what I can do? Feedback would be much appreciated.

Thank you,
Anjali

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10 years 4 months ago #3519 by Clement
Replied by Clement on topic Accessing the DSSP binary
I think you need to give the complete path to the executable, e.g. the executable itself.

If this doesn't work, could you copy/paste the error message here?

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10 years 3 months ago #3520 by anjali
Replied by anjali on topic Accessing the DSSP binary
Hi Clement,

Thanks for your reply.

I don't really know what you mean by "calling the executable" because in my dssp library, there doesn't seem to be an executable file there..?

In either case, this is the error message I receive:
a4gopal@z87-pro:/scratch/a4gopal/protein$ python martinize.py -f 1UBQ.pdb -o system.top -x cg_1UBQ.pdb -dssp /scratch/a4gopal/dssp -p backbone -ff martini22
INFO       MARTINIZE, script version 2.4
INFO       If you use this script please cite:
INFO       de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO       Chain termini will be charged
INFO       Residues at chain brakes will not be charged
INFO       The martini22 forcefield will be used.
INFO       Local elastic bonds will be used for extended regions.
INFO       Position restraints will be generated.
WARNING    Position restraints are only enabled if -DPOSRES is set in the MDP file
INFO       Read input structure from file.
INFO       Input structure is a PDB file.
INFO       Found 2 chains:
INFO          1:   A (Protein), 602 atoms in 76 residues.
INFO          2:   A (Water), 58 atoms in 58 residues.
INFO       Removing 58 water molecules (chain A).
INFO       Total size of the system: 76 residues.
ERROR      A problem occured calling /scratch/a4gopal/dssp.

Thank you,
Anjali

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10 years 3 months ago #3521 by anjali
Replied by anjali on topic Accessing the DSSP binary
Actually, I finally did end up getting this working!

So, solution:
- Basically, I downloaded the binary and not the executable, as you suggested
- So I downloaded the executable, used chmod to change the permissions
chmod +x dsspcmbi
- Then I was able to run this command:
python martinize.py -f 2MAG.pdb -o system.top -x cg_2MAG.pdb -dssp ../dssp/dsspcmbi -p backbone -ff martini22

Thank you very much for all your help! :)

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7 years 11 months ago #5709 by jonasori
Replied by jonasori on topic Accessing the DSSP binary
This is very late, but where did you download the executable from? I think I'm in the same boat, right up to the point where the OP solved the problem.

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4 years 1 month ago #8518 by huynhqu1
Replied by huynhqu1 on topic Accessing the DSSP binary
Hi everyone,

Like Anjali and Jonasori, I have the exact same problem with dssp when I use martinize.py.

Does anyone know where and how I can download the dssp executable? I followed this website to do so swift.cmbi.umcn.nl/gv/dssp/ , but I could not find (or did not know where and how to download) the executable.

I would truly appreciate your kind help! Thank you!

Quang

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4 years 1 month ago #8520 by riccardo
Replied by riccardo on topic Accessing the DSSP binary
I also couldn't find the executable on that page (only the source, via that webpage, then GitHub github.com/cmbi/hssp/releases ). By the way, did you try to install it from source (instructions as README.md inside the source.zip you can download from github.com/cmbi/hssp/releases )?
Btw, not sure what the difference is w.r.t. github.com/cmbi/dssp .

Here, I think I found an executable:
redmine.gromacs.org/attachments/792/dsspcmbi

But I guess it should be easier than this and I am missing something..

Hope this helps though

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4 years 1 month ago #8522 by huynhqu1
Replied by huynhqu1 on topic Accessing the DSSP binary
Thank you so much Riccardo!

I tried to install it from source following instructions given README.md, but I get an error about "aclocal: command not found" when I execute ./autogen.sh (I guess likely because I do not have pre-requisites on the CentOS system).

Regarding the dssp executable you found, I downloaded it and tried it with martinize.py. Unfortunately, I still get the same error (a problem occured calling ...)

Did you get the -dssp flag to work with martinize.py? Thank you!

Best,
Quang

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9 months 3 weeks ago #9670 by Dheeraj
Replied by Dheeraj on topic Accessing the DSSP binary
For martinize2 with vermouth (installed by "pip install vermouth" in a conda env), dssp 3.0.0 can be installed by "conda install -c salilab dssp".
"which mkdssp" will tell you where it is located. It works for martinizing to Martini3. I assume it will for Martini2 as well. Worst case, I have the binary for DSSP 2.0.4 on my github (which I have used to martinize to Martini 2 ff) - github.com/DJ004/MolDynamics_gromacs/blo...ssp-2.0.4-linux-i386

Hope this helps.

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