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backward.py problem determining mapping coordinates
- molayemi
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4 years 3 months ago #8399
by molayemi
Replied by molayemi on topic backward.py problem determining mapping coordinates
Hi,
Were you able to fix this backmapping error? I have the same problem. I will appreciate it if you can share how you fixed this.
Best,
maryam
Were you able to fix this backmapping error? I have the same problem. I will appreciate it if you can share how you fixed this.
Best,
maryam
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- tsjerk
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4 years 3 months ago #8404
by tsjerk
Replied by tsjerk on topic backward.py problem determining mapping coordinates
Hi Maryam,
Please send me the coarse grain structure and the complete target topology. I think I understand the error and need to check.
Best,
Tsjerk
Please send me the coarse grain structure and the complete target topology. I think I understand the error and need to check.
Best,
Tsjerk
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- molayemi
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4 years 3 months ago #8405
by molayemi
Replied by molayemi on topic backward.py problem determining mapping coordinates
Hi Tsjerk,
Thanks for replying. Can you please send me your email address so I can send them to you?
Thanks for replying. Can you please send me your email address so I can send them to you?
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- riccardo
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4 years 3 months ago #8406
by riccardo
Replied by riccardo on topic backward.py problem determining mapping coordinates
Tsjerk's email:
t.a.wassenaar [at] rug.nl
t.a.wassenaar [at] rug.nl
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- molayemi
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4 years 3 months ago #8407
by molayemi
Replied by molayemi on topic backward.py problem determining mapping coordinates
Thanks Riccardo.
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- molayemi
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4 years 1 month ago #8463
by molayemi
Replied by molayemi on topic backward.py problem determining mapping coordinates
Dear all,
I am trying to backmap Heme from CG to AA using the backward.py script but I keep getting error message ( will paste below), can anyone help or tell me how to fix this?
Non-invertable box. Not able to unbreak molecules...
Error reading charmm27 to martini mapping for TOCL2 (file: /home/maryam/testheme/Mapping/phe.amber.map).
Error reading charmm36 to martini mapping for TOCL2 (file: /home/maryam/testheme/Mapping/phe.amber.map).
Error reading slipids to martini mapping for TOCL2 (file: /home/maryam/testheme/Mapping/phe.amber.map).
Error reading amber to martini mapping for TOCL2 (file: /home/maryam/testheme/Mapping/phe.amber.map).
Error reading charmm27 to martini mapping for DOPE (file: /home/maryam/testheme/Mapping/ala.charmm36.map).
Error reading charmm36 to martini mapping for DOPE (file: /home/maryam/testheme/Mapping/ala.charmm36.map).
Error reading slipids to martini mapping for DOPE (file: /home/maryam/testheme/Mapping/ala.charmm36.map).
Error reading amber to martini mapping for DOPE (file: /home/maryam/testheme/Mapping/ala.charmm36.map).
Error reading charmm27 to martini mapping for POPG (file: /home/maryam/testheme/Mapping/lys.amber.map).
Error reading charmm36 to martini mapping for POPG (file: /home/maryam/testheme/Mapping/lys.amber.map).
Error reading slipids to martini mapping for POPG (file: /home/maryam/testheme/Mapping/lys.amber.map).
Error reading amber to martini mapping for POPG (file: /home/maryam/testheme/Mapping/lys.amber.map).
Error reading charmm27 to martini mapping for DOPG (file: /home/maryam/testheme/Mapping/popc.alex.map).
Error reading charmm36 to martini mapping for DOPG (file: /home/maryam/testheme/Mapping/popc.alex.map).
Error reading slipids to martini mapping for DOPG (file: /home/maryam/testheme/Mapping/popc.alex.map).
Error reading amber to martini mapping for DOPG (file: /home/maryam/testheme/Mapping/popc.alex.map).
Error reading charmm27 to martini mapping for DOPS (file: /home/maryam/testheme/Mapping/ser.gromos.map).
Error reading charmm36 to martini mapping for DOPS (file: /home/maryam/testheme/Mapping/ser.gromos.map).
Error reading slipids to martini mapping for DOPS (file: /home/maryam/testheme/Mapping/ser.gromos.map).
Error reading amber to martini mapping for DOPS (file: /home/maryam/testheme/Mapping/ser.gromos.map).
Residues defined for transformation from martini to charmm22star:
dict_keys([])
None
Traceback (most recent call last):
File "/home/maryam/testheme/backward.py", line 957, in <module>
raise ValueError("Residue not found in mapping dictionary: %s\n"%resn)
ValueError: Residue not found in mapping dictionary: HEM
Best,
Maryam
I am trying to backmap Heme from CG to AA using the backward.py script but I keep getting error message ( will paste below), can anyone help or tell me how to fix this?
Non-invertable box. Not able to unbreak molecules...
Error reading charmm27 to martini mapping for TOCL2 (file: /home/maryam/testheme/Mapping/phe.amber.map).
Error reading charmm36 to martini mapping for TOCL2 (file: /home/maryam/testheme/Mapping/phe.amber.map).
Error reading slipids to martini mapping for TOCL2 (file: /home/maryam/testheme/Mapping/phe.amber.map).
Error reading amber to martini mapping for TOCL2 (file: /home/maryam/testheme/Mapping/phe.amber.map).
Error reading charmm27 to martini mapping for DOPE (file: /home/maryam/testheme/Mapping/ala.charmm36.map).
Error reading charmm36 to martini mapping for DOPE (file: /home/maryam/testheme/Mapping/ala.charmm36.map).
Error reading slipids to martini mapping for DOPE (file: /home/maryam/testheme/Mapping/ala.charmm36.map).
Error reading amber to martini mapping for DOPE (file: /home/maryam/testheme/Mapping/ala.charmm36.map).
Error reading charmm27 to martini mapping for POPG (file: /home/maryam/testheme/Mapping/lys.amber.map).
Error reading charmm36 to martini mapping for POPG (file: /home/maryam/testheme/Mapping/lys.amber.map).
Error reading slipids to martini mapping for POPG (file: /home/maryam/testheme/Mapping/lys.amber.map).
Error reading amber to martini mapping for POPG (file: /home/maryam/testheme/Mapping/lys.amber.map).
Error reading charmm27 to martini mapping for DOPG (file: /home/maryam/testheme/Mapping/popc.alex.map).
Error reading charmm36 to martini mapping for DOPG (file: /home/maryam/testheme/Mapping/popc.alex.map).
Error reading slipids to martini mapping for DOPG (file: /home/maryam/testheme/Mapping/popc.alex.map).
Error reading amber to martini mapping for DOPG (file: /home/maryam/testheme/Mapping/popc.alex.map).
Error reading charmm27 to martini mapping for DOPS (file: /home/maryam/testheme/Mapping/ser.gromos.map).
Error reading charmm36 to martini mapping for DOPS (file: /home/maryam/testheme/Mapping/ser.gromos.map).
Error reading slipids to martini mapping for DOPS (file: /home/maryam/testheme/Mapping/ser.gromos.map).
Error reading amber to martini mapping for DOPS (file: /home/maryam/testheme/Mapping/ser.gromos.map).
Residues defined for transformation from martini to charmm22star:
dict_keys([])
None
Traceback (most recent call last):
File "/home/maryam/testheme/backward.py", line 957, in <module>
raise ValueError("Residue not found in mapping dictionary: %s\n"%resn)
ValueError: Residue not found in mapping dictionary: HEM
Best,
Maryam
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- riccardo
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4 years 1 month ago #8464
by riccardo
Replied by riccardo on topic backward.py problem determining mapping coordinates
There's a few things I can spot:
1. You don't have a mapping file for HEM, do you? This is a file called, for example, heme.gromos.map which must placed in the Mapping directory.
2. "Non-invertable box. Not able to unbreak molecules... " not sure about this error message; I remember I was getting it a long time ago. Try making your simulation box "whole" (i.e., gmx trjconv -f traj.xtc -o traj-whole.xtc -pbc whole ...) and see if you get rid of it.
3. Not sure what all the "Error reading ..... to martini mapping for ..... (file: /home/maryam/testheme/Mapping/phe.amber.map)." are about. I think the recommended choice is to use the GitHub version of backward ( github.com/Tsjerk/Backward ) so please download that if you aren't using that version yet.
1. You don't have a mapping file for HEM, do you? This is a file called, for example, heme.gromos.map which must placed in the Mapping directory.
2. "Non-invertable box. Not able to unbreak molecules... " not sure about this error message; I remember I was getting it a long time ago. Try making your simulation box "whole" (i.e., gmx trjconv -f traj.xtc -o traj-whole.xtc -pbc whole ...) and see if you get rid of it.
3. Not sure what all the "Error reading ..... to martini mapping for ..... (file: /home/maryam/testheme/Mapping/phe.amber.map)." are about. I think the recommended choice is to use the GitHub version of backward ( github.com/Tsjerk/Backward ) so please download that if you aren't using that version yet.
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- molayemi
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4 years 1 month ago #8466
by molayemi
Replied by molayemi on topic backward.py problem determining mapping coordinates
Dear Riccardo,
Thanks for your response. Yes you are right, I do not have the hem.map file, I just assumed it was going to be available in the mapping directory. Please, can you direct me to where/how can I get one? Do I have to make one myself? I tried reading the mapping part of the tutorial to see if I can try make one myself but I have not really gotten a hang of it. For the thir error, yes I am using the Github version of the backward script.
Thanks for your response. Yes you are right, I do not have the hem.map file, I just assumed it was going to be available in the mapping directory. Please, can you direct me to where/how can I get one? Do I have to make one myself? I tried reading the mapping part of the tutorial to see if I can try make one myself but I have not really gotten a hang of it. For the thir error, yes I am using the Github version of the backward script.
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- riccardo
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4 years 1 month ago #8467
by riccardo
Replied by riccardo on topic backward.py problem determining mapping coordinates
Then the problem is really the missing mapping file for heme.
By reading Backward's paper and the tutorial you should have understood the syntax of a mapping file. However, there is indeed a bit of work involved in making a mapping file for a complex molecule such as a heme group. Recently, Jonathan Barnoud developed a useful tool which can facilitate your life very much: jbarnoud.github.io/cgbuilder/ (GitHub repo here: github.com/jbarnoud/cgbuilder ). Not much documentation is available (yet), but the tool is pretty intuitive: you go to jbarnoud.github.io/cgbuilder/ , you upload the atomistic PDB of your heme (the PDB which corresponds to your atomistic force field - you have that, right?), and then you map your heme to CG resolution by clicking on the atoms and creating beads as you go (it's pretty intuitive; just make sure to use the same bead ordering as in your CG itp!). Now, the pretty neat functionality of Jonathan's cgbuilder is the fact that it allows you to download not only the atomistic-to-CG.ndx file but also the CG-to-atomistic.map file! The latter may be, at least, a very good initial guess for your mapping file; at best, it'll work as it is without further refinements. Note that by "refinements" here I mean the *geometrical modifiers* discussed by Wassenaar et al. in the Backward paper.
Good luck and let me know if you have further questions. Also, it might be wise to practice a little first with a smaller molecule.
By reading Backward's paper and the tutorial you should have understood the syntax of a mapping file. However, there is indeed a bit of work involved in making a mapping file for a complex molecule such as a heme group. Recently, Jonathan Barnoud developed a useful tool which can facilitate your life very much: jbarnoud.github.io/cgbuilder/ (GitHub repo here: github.com/jbarnoud/cgbuilder ). Not much documentation is available (yet), but the tool is pretty intuitive: you go to jbarnoud.github.io/cgbuilder/ , you upload the atomistic PDB of your heme (the PDB which corresponds to your atomistic force field - you have that, right?), and then you map your heme to CG resolution by clicking on the atoms and creating beads as you go (it's pretty intuitive; just make sure to use the same bead ordering as in your CG itp!). Now, the pretty neat functionality of Jonathan's cgbuilder is the fact that it allows you to download not only the atomistic-to-CG.ndx file but also the CG-to-atomistic.map file! The latter may be, at least, a very good initial guess for your mapping file; at best, it'll work as it is without further refinements. Note that by "refinements" here I mean the *geometrical modifiers* discussed by Wassenaar et al. in the Backward paper.
Good luck and let me know if you have further questions. Also, it might be wise to practice a little first with a smaller molecule.
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