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Backward.py for glycolipid
- Akshay
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9 years 2 months ago #4466
by Akshay
Backward.py for glycolipid was created by Akshay
Hello,
I have been trying to simulate a glycolipid(GM1): DPPC membrane. I've managed to build the membrane. But the backward package does not contain the .map files for the glycolipids.
The paper detailing the parameterization of GM1 does not seem to provide details of how the tail groups of GM1 are built.
Any suggestions on back-mapping my DPPC:GM1 membrane would be appreciated :)
Thanks
I have been trying to simulate a glycolipid(GM1): DPPC membrane. I've managed to build the membrane. But the backward package does not contain the .map files for the glycolipids.
The paper detailing the parameterization of GM1 does not seem to provide details of how the tail groups of GM1 are built.
Any suggestions on back-mapping my DPPC:GM1 membrane would be appreciated :)
Thanks
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- hadiseh
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9 years 2 weeks ago #4510
by hadiseh
Replied by hadiseh on topic Backward.py for glycolipid
Hello
I have the same problem for making .map file for DDM.
I really appreciate if some one provide more detailed information on how to make such files.
Thanks
I have the same problem for making .map file for DDM.
I really appreciate if some one provide more detailed information on how to make such files.
Thanks
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- helgi
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9 years 2 weeks ago #4512
by helgi
Replied by helgi on topic Backward.py for glycolipid
Sorry for a slow response, we have been working with GM1 but didn’t get around to making the backmapping file until recently. Ruo-Xu Gu from Peter Tielemans lab made this one; here it is linked through Dropbox:
www.dropbox.com/sh/y2c22dip64qbk89/AAAEZ...1658mJxPy19V-9a?dl=0
We are currently reorganizing the martini lipid parameter section of our website and will add it there when we are done.
Also in the dropbox link is a GROMOS AA parameter file for this GM1 that Cesar Lopez put together, with one extra dihedral added to the very end by Ruo-Xu Gu to help backmap into the correct structure. Normally you can get the correct backmapped structures by adding helping rules to the .map file to guide the initial atom placement, but in this case it was easier to add an extra dihedral to the AA FF used in the minimization.
Hope this one helps,
Cheers,
- Helgi
www.dropbox.com/sh/y2c22dip64qbk89/AAAEZ...1658mJxPy19V-9a?dl=0
We are currently reorganizing the martini lipid parameter section of our website and will add it there when we are done.
Also in the dropbox link is a GROMOS AA parameter file for this GM1 that Cesar Lopez put together, with one extra dihedral added to the very end by Ruo-Xu Gu to help backmap into the correct structure. Normally you can get the correct backmapped structures by adding helping rules to the .map file to guide the initial atom placement, but in this case it was easier to add an extra dihedral to the AA FF used in the minimization.
Hope this one helps,
Cheers,
- Helgi
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- helgi
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9 years 2 weeks ago #4513
by helgi
Replied by helgi on topic Backward.py for glycolipid
Sadly I don't know of anyone that has made a .map file for DDM but it should not be so hard to make. E.g. see the Going Backward paper:
Wassenaar, T. A., Pluhackova, K., Böckmann, R. A., Marrink, S. J., and Tieleman, D. P. (2014) Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. J. Chem. Theory Comput. 10, 676–690.
And our backwards tutorial:
cgmartini.nl/cgmartini/index.php/others#Backward
If your AA force field enforces the correct maltose geometry you should be fine with just specifying what atoms map to what beads. If not, you might need to provide some stereochemical specifically, you can see examples of how to add those in the tutorial and in many of the other .map files provided in backwards.
Cheers,
- Helgi
Wassenaar, T. A., Pluhackova, K., Böckmann, R. A., Marrink, S. J., and Tieleman, D. P. (2014) Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. J. Chem. Theory Comput. 10, 676–690.
And our backwards tutorial:
cgmartini.nl/cgmartini/index.php/others#Backward
If your AA force field enforces the correct maltose geometry you should be fine with just specifying what atoms map to what beads. If not, you might need to provide some stereochemical specifically, you can see examples of how to add those in the tutorial and in many of the other .map files provided in backwards.
Cheers,
- Helgi
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- hadiseh
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9 years 1 week ago #4520
by hadiseh
Replied by hadiseh on topic Backward.py for glycolipid
Thanks for your reply, it really helped.
Now, the problem is I have problem in writing [out]/[chairal]/ part of the .map file.
I have Trehalose and glucose .map files to get some idea of them as the subpart of my DDM molecule.
I had some idea of the glucose [chiral]/[out] .map files but I got lost in Trehalose [out]/[chiral] part.
to be more clear, I want to backmap a system containing detergent(DDM) around protein in a solvent(water). I have .itp files of AA DDM and CG DDM.
I have another question, does it matter how we name the atoms in this file? should be similarity between .itp file and .map files?
for example, in my .itp files atoms are named as "oh, Os , ho" but in the .map files I have for glucose and trehalose the atoms are named like HO41, O1
so, could you give me some hint on that?
Thanks
P.S I am a physics student ...
Now, the problem is I have problem in writing [out]/[chairal]/ part of the .map file.
I have Trehalose and glucose .map files to get some idea of them as the subpart of my DDM molecule.
I had some idea of the glucose [chiral]/[out] .map files but I got lost in Trehalose [out]/[chiral] part.
to be more clear, I want to backmap a system containing detergent(DDM) around protein in a solvent(water). I have .itp files of AA DDM and CG DDM.
I have another question, does it matter how we name the atoms in this file? should be similarity between .itp file and .map files?
for example, in my .itp files atoms are named as "oh, Os , ho" but in the .map files I have for glucose and trehalose the atoms are named like HO41, O1
so, could you give me some hint on that?
Thanks
P.S I am a physics student ...
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