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conversion from atomic model to CG model for lipid
- wenchangyu2006
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13 years 8 months ago #404
by wenchangyu2006
conversion from atomic model to CG model for lipid was created by wenchangyu2006
Hi all,
Does anybody know tools that can convert atomic model to CG model for lipids like POPC,POPE?
I have a pre-equilibrated system with protein and membrane POPC inside. What I want is to convert this system directly into CG model. I'm sure there will be no problem for protein conversion but I think not for lipid since there is no data for lipid in the file cg-2.1.dat or AA-2.1.dat when using script pdb2CGpdb-2.1.f . I appreciate if there are some suggestions.
Best,
Wenchang
Does anybody know tools that can convert atomic model to CG model for lipids like POPC,POPE?
I have a pre-equilibrated system with protein and membrane POPC inside. What I want is to convert this system directly into CG model. I'm sure there will be no problem for protein conversion but I think not for lipid since there is no data for lipid in the file cg-2.1.dat or AA-2.1.dat when using script pdb2CGpdb-2.1.f . I appreciate if there are some suggestions.
Best,
Wenchang
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13 years 7 months ago #408
by xavier
Replied by xavier on topic conversion from atomic model to CG model for lipid
Dear Wenchang,
There is no direct tool to convert the type of system you mention from an atomistic to a CG system. However you can transform the protein and lipid system separately and put them back together while they are CG.
The protein using the script you mention is fine.
For the lipids you can use the reverse transformation tool for which you'll need to define the AA->CG mapping in your
AA topology and also have the CG topology in hand.
Check the reverse transformation tutorial on the website.
Best,
XAvier.
There is no direct tool to convert the type of system you mention from an atomistic to a CG system. However you can transform the protein and lipid system separately and put them back together while they are CG.
The protein using the script you mention is fine.
For the lipids you can use the reverse transformation tool for which you'll need to define the AA->CG mapping in your
AA topology and also have the CG topology in hand.
Check the reverse transformation tutorial on the website.
Best,
XAvier.
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- wenchangyu2006
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13 years 7 months ago #412
by wenchangyu2006
Replied by wenchangyu2006 on topic conversion from atomic model to CG model for lipid
Thanks,XAvier. Actually What I want is a larger membrance with 256 lipids on each layer, meaning I can duplicate the 128 lipid bilayer 4 times larger. What I did is to use genconf command:
genconf -f pope_bilayer.gro -o expend.gro -nbox 2 2 1
When I continue to do minimization everything is fine, but with "segmentation fault" error when I goto equilibration. I think there are some overlaps between the parts I duplicated and this gives out the error.
Do you have any way to generate the lipid layer I want (256 lipids on each layer). I mean, on the website there are several not big enough lipid layer.
genconf -f pope_bilayer.gro -o expend.gro -nbox 2 2 1
When I continue to do minimization everything is fine, but with "segmentation fault" error when I goto equilibration. I think there are some overlaps between the parts I duplicated and this gives out the error.
Do you have any way to generate the lipid layer I want (256 lipids on each layer). I mean, on the website there are several not big enough lipid layer.
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13 years 7 months ago #415
by xavier
Replied by xavier on topic conversion from atomic model to CG model for lipid
Well the way you did should be perfectly fine.
Did you think of changing the box size the new gro file. The x and y dimensions should be doubled :))
Did you think of changing the box size the new gro file. The x and y dimensions should be doubled :))
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13 years 7 months ago #416
by wenchangyu2006
Replied by wenchangyu2006 on topic conversion from atomic model to CG model for lipid
The box size of the new gro files will be changed by the proram genconf, which I checked correct after using command
genconf -f pope_bilayer.gro -o pope_bilayer_512.gro -nbox 2 2 1
When I do the minimization with mdrun, error messages comes out:
Reading file em.tpr, VERSION 4.5-beta2 (double precision)
Starting 8 threads
Making 2D domain decomposition 2 x 4 x 1
Segmentation fault
In the end of the log file syas:
Removing pbc first time
Linking all bonded interactions to atoms
The initial number of communication pulses is: X 1 Y 1
The initial domain decomposition cell size is: X 6.01 nm Y 3.16 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.400 nm
two-body bonded interactions (-rdd) 1.400 nm
multi-body bonded interactions (-rdd) 1.400 nm
just stuck here and quit. Do you have any suggestions about this? Thanks a lot.
genconf -f pope_bilayer.gro -o pope_bilayer_512.gro -nbox 2 2 1
When I do the minimization with mdrun, error messages comes out:
Reading file em.tpr, VERSION 4.5-beta2 (double precision)
Starting 8 threads
Making 2D domain decomposition 2 x 4 x 1
Segmentation fault
In the end of the log file syas:
Removing pbc first time
Linking all bonded interactions to atoms
The initial number of communication pulses is: X 1 Y 1
The initial domain decomposition cell size is: X 6.01 nm Y 3.16 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.400 nm
two-body bonded interactions (-rdd) 1.400 nm
multi-body bonded interactions (-rdd) 1.400 nm
just stuck here and quit. Do you have any suggestions about this? Thanks a lot.
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13 years 7 months ago #417
by wenchangyu2006
Replied by wenchangyu2006 on topic conversion from atomic model to CG model for lipid
Just add more information about the mdp file, which is directly from the tutorial website.
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13 years 7 months ago #418
by wenchangyu2006
Replied by wenchangyu2006 on topic conversion from atomic model to CG model for lipid
Until now everything goes well after I pay more attention to the max force and the potential energy value right after minimization. I may report new problems :)
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