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Martinize.py on large protein
- pela3247
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11 years 3 months ago #1360
by pela3247
Martinize.py on large protein was created by pela3247
Dear all
I've worked my way through the tutorials with good results, and now I am trying to use the martinize.py (v 2.2) script on a protein of my own. My command line is the following:
python martinize.py -f protein_chainA.pdb -o topol_chainA.top -x cg_chainA.pdb -dssp /Users/per/source/dssp/dsspcmbi -p backbone
And then some output is reported on screen:
INFO MARTINIZE, script version 2.2
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 martini21 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 1 chains:
INFO 1: (Protein), 11893 atoms in 747 residues.
INFO Total size of the system: 747 residues.
But then nothing happens. As I said, I've used the script on smaller proteins, but for my research I need to work on this particular protein. Is there a limit to the size of proteins that can be handled by martinize.py?
I can probably work around this with the g_fg2cg tool, but since I'm not using any of the gromos forcefields that would require a lot of tedious conversions. Any ideas about what could be going wrong? The script has been running now for about 30 mins...
Thanks
/Per
I've worked my way through the tutorials with good results, and now I am trying to use the martinize.py (v 2.2) script on a protein of my own. My command line is the following:
python martinize.py -f protein_chainA.pdb -o topol_chainA.top -x cg_chainA.pdb -dssp /Users/per/source/dssp/dsspcmbi -p backbone
And then some output is reported on screen:
INFO MARTINIZE, script version 2.2
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 martini21 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 1 chains:
INFO 1: (Protein), 11893 atoms in 747 residues.
INFO Total size of the system: 747 residues.
But then nothing happens. As I said, I've used the script on smaller proteins, but for my research I need to work on this particular protein. Is there a limit to the size of proteins that can be handled by martinize.py?
I can probably work around this with the g_fg2cg tool, but since I'm not using any of the gromos forcefields that would require a lot of tedious conversions. Any ideas about what could be going wrong? The script has been running now for about 30 mins...
Thanks
/Per
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- djurre
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11 years 3 months ago #1361
by djurre
Replied by djurre on topic Martinize.py on large protein
I've never seen a size limitation of martinize.py, but I also never tried to push it. How many residues are we talking about? If it is a multi chain protein you could try to do it chain by chain.
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- pela3247
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11 years 3 months ago #1362
by pela3247
Replied by pela3247 on topic Martinize.py on large protein
Thanks for your answer!
This is a protein with two chains. I tried the whole thing first, and then split it up into individual chains, with the same result.
However, just as I was reading your reply, I tried to run dssp first manually, and then feed the ss-file into martinize. That seems to have done the trick (as opposed to using the -dssp switch). Not sure why though, and I am going to check if I get the correct results. Will report back!
Thanks
/Per
Edit: PS. There are about 1400 residues in total, with roughly 700 in each chain.
This is a protein with two chains. I tried the whole thing first, and then split it up into individual chains, with the same result.
However, just as I was reading your reply, I tried to run dssp first manually, and then feed the ss-file into martinize. That seems to have done the trick (as opposed to using the -dssp switch). Not sure why though, and I am going to check if I get the correct results. Will report back!
Thanks
/Per
Edit: PS. There are about 1400 residues in total, with roughly 700 in each chain.
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- pela3247
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11 years 3 months ago #1364
by pela3247
Replied by pela3247 on topic Martinize.py on large protein
Hello again
Not sure why, but running dssp manually on each chain separately, and then using the martinize script with the -ss option does the trick in my case. I post the method here and hope that it might be useful for someone else.
Thanks
/Per
Not sure why, but running dssp manually on each chain separately, and then using the martinize script with the -ss option does the trick in my case. I post the method here and hope that it might be useful for someone else.
Thanks
/Per
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