- Posts: 103
Using insane.py
- tsjerk
-
- Offline
- Expert Boarder
Less
More
10 years 5 months ago #2623
by tsjerk
Replied by tsjerk on topic Using insane.py
Good :) If you need to tune the number of lipids inside the protein, you can also play with the -fudge parameter. Making the protein more fudgy will allow more overlap with lipids.
Please Log in or Create an account to join the conversation.
- Rajat Desikan
-
Topic Author
- Offline
- Expert Boarder
Less
More
- Posts: 90
10 years 5 months ago #2624
by Rajat Desikan
Replied by Rajat Desikan on topic Using insane.py
Thanks! That is useful to know. I was thinking of decreasing area per lipid to play around with the lipids in the protein interior, but this is more local and probably gives me a better handle :)
Please Log in or Create an account to join the conversation.
- visvaldas
-
- Visitor
10 years 4 months ago #3025
by visvaldas
Replied by visvaldas on topic Using insane.py
I think there is an error in the generation of box vectors using -pbc optimal.
I used:
python ~/bin/insane.py -f prot_cg.pdb -l POPC -o assembled.gro -center -pbc optimal -p out.top
and the last line in the gro file was:
10.99450 9.52152 0.00000 0.00000 0.00000 5.49725 0.00000 5.49725 3.17384
It took me some time to realize the Z dimension was lacking (vmd with "pbc box -on" showd a flat pbc box).
After some playing around I found that one number is missing, the correct box should be:
10.99450 9.52152 8.97697 0.00000 0.00000 5.49725 0.00000 5.49725 3.17384
The missing number was 8.97697 which is (1/6)*sqrt(6)*d according to GROMACS manual.
Best regards,
Visvaldas
I used:
python ~/bin/insane.py -f prot_cg.pdb -l POPC -o assembled.gro -center -pbc optimal -p out.top
and the last line in the gro file was:
10.99450 9.52152 0.00000 0.00000 0.00000 5.49725 0.00000 5.49725 3.17384
It took me some time to realize the Z dimension was lacking (vmd with "pbc box -on" showd a flat pbc box).
After some playing around I found that one number is missing, the correct box should be:
10.99450 9.52152 8.97697 0.00000 0.00000 5.49725 0.00000 5.49725 3.17384
The missing number was 8.97697 which is (1/6)*sqrt(6)*d according to GROMACS manual.
Best regards,
Visvaldas
Please Log in or Create an account to join the conversation.
- tsjerk
-
- Offline
- Expert Boarder
Less
More
- Posts: 103
10 years 4 months ago - 10 years 4 months ago #3045
by tsjerk
Replied by tsjerk on topic Using insane.py
Thanks for reporting this.
Can you check if it still happens with my development version? www.bioinf.nl/~tsjerk/insane.html
Can you check if it still happens with my development version? www.bioinf.nl/~tsjerk/insane.html
Last edit: 10 years 4 months ago by tsjerk.
Please Log in or Create an account to join the conversation.
- visvaldas
-
- Visitor
10 years 4 months ago #3057
by visvaldas
Replied by visvaldas on topic Using insane.py
Sorry Tsjerk, the link doesn't work...
Please Log in or Create an account to join the conversation.
- tsjerk
-
- Offline
- Expert Boarder
Less
More
- Posts: 103
10 years 4 months ago #3058
by tsjerk
Replied by tsjerk on topic Using insane.py
Try "save link as". That works for me...
Please Log in or Create an account to join the conversation.
- visvaldas
-
- Visitor
10 years 4 months ago #3059
by visvaldas
Replied by visvaldas on topic Using insane.py
The links is saved as an html file with the following content:
Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator, This email address is being protected from spambots. You need JavaScript enabled to view it. and inform them of the time the error occurred, and anything you might have done that may have caused the error.
More information about this error may be available in the server error log.
Visvaldas
Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator, This email address is being protected from spambots. You need JavaScript enabled to view it. and inform them of the time the error occurred, and anything you might have done that may have caused the error.
More information about this error may be available in the server error log.
Visvaldas
Please Log in or Create an account to join the conversation.
- tsjerk
-
- Offline
- Expert Boarder
Less
More
- Posts: 103
10 years 4 months ago #3060
by tsjerk
Replied by tsjerk on topic Using insane.py
Sorry about that. Will check with the webmaster there. Put the script here:
nmr.chem.uu.nl/~tsjerk/insane.py
There it does work :p
There it does work :p
Please Log in or Create an account to join the conversation.
- visvaldas
-
- Visitor
10 years 4 months ago #3061
by visvaldas
Replied by visvaldas on topic Using insane.py
it works, fantastic! Thanks!
best regards,
Visvaldas
best regards,
Visvaldas
Please Log in or Create an account to join the conversation.
- tsjerk
-
- Offline
- Expert Boarder
Less
More
- Posts: 103
10 years 4 months ago #3062
by tsjerk
Replied by tsjerk on topic Using insane.py
Does it solve the problem with the box?
Please Log in or Create an account to join the conversation.
- visvaldas
-
- Visitor
10 years 4 months ago #3066
by visvaldas
Replied by visvaldas on topic Using insane.py
Well, I meant the box works, not only the link!
Best,
Vis
Best,
Vis
Please Log in or Create an account to join the conversation.
- flaviyan
-
- Offline
- Senior Boarder
Less
More
- Posts: 54
10 years 3 months ago #3436
by flaviyan
Replied by flaviyan on topic Using insane.py
Hi Admin,
I greatly appreciate the work and effort put on by the martini group. I am using the Martini 2.4 script and trying to simulate a protein(homooligomer) in lipid bi-layer and trying to use the insane.py script for generating the lipid bi-layer. My question is whether to coarse grain the protein and build the bi-layer or build the bi-layer around the protein and then CG the entire file? I am not sure which one should I use.
I greatly appreciate the work and effort put on by the martini group. I am using the Martini 2.4 script and trying to simulate a protein(homooligomer) in lipid bi-layer and trying to use the insane.py script for generating the lipid bi-layer. My question is whether to coarse grain the protein and build the bi-layer or build the bi-layer around the protein and then CG the entire file? I am not sure which one should I use.
Please Log in or Create an account to join the conversation.
- Clement
-
- Offline
- Admin
Less
More
- Posts: 211
10 years 3 months ago #3437
by Clement
Replied by Clement on topic Using insane.py
martinize.py and others will work on the different components (lipids, proteins, ...) separately. Does not really make sense to waste time building an atomistic system beforehand.
And as far as I know, insane.py works with CG stuff...
CG first, build after.
And as far as I know, insane.py works with CG stuff...
CG first, build after.
Please Log in or Create an account to join the conversation.
- flaviyan
-
- Offline
- Senior Boarder
Less
More
- Posts: 54
10 years 3 months ago #3438
by flaviyan
Replied by flaviyan on topic Using insane.py
Thank you for your replies,
I have another doubt with insane.py what dose the -fudge option actually do, I see that it takes float parameters but i am not sure of the significance.
I have another doubt with insane.py what dose the -fudge option actually do, I see that it takes float parameters but i am not sure of the significance.
Please Log in or Create an account to join the conversation.
- tsjerk
-
- Offline
- Expert Boarder
Less
More
- Posts: 103
10 years 3 months ago #3439
by tsjerk
Replied by tsjerk on topic Using insane.py
The option -fudge sets the fudge factor for proteins. Whether a cell is available for placement of a lipid depends on the occupancy by protein particles. A fudge factor of 0.0 means that any protein particle marks the cell as occupied, while a fudge factor of 1.0 will always cause a lipid to be placed, regardless of the number of protein particles.
Please Log in or Create an account to join the conversation.
- flaviyan
-
- Offline
- Senior Boarder
Less
More
- Posts: 54
10 years 3 months ago #3440
by flaviyan
Replied by flaviyan on topic Using insane.py
Thanks for the explanation. So the cell in question is of the dimension equivalent to the dimensions of the lipid we are using. if so what would be an optimal value of the fudge factor.
Please Log in or Create an account to join the conversation.
- tsjerk
-
- Offline
- Expert Boarder
Less
More
- Posts: 103
10 years 3 months ago #3441
by tsjerk
Replied by tsjerk on topic Using insane.py
The default value is 0.1. That usually does pretty well. If you find that there is too much space around the protein, you can raise the value. This is particularly useful when you have ring-shaped molecules, where you use -ring to allow placement of lipids inside. Within, the number of lipids cannot change, so you can use -fudge to alter the number of lipids actually placed there.
Please Log in or Create an account to join the conversation.
- flaviyan
-
- Offline
- Senior Boarder
Less
More
- Posts: 54
10 years 3 months ago #3474
by flaviyan
Replied by flaviyan on topic Using insane.py
Hi,
I am using the insane.py script to build a CG membrane protein system which has 2 bilayers in it. due to the complexity involved I built the system in 2 steps
1. build the membrane around the protein using insane.py without any solvent and assemble the system using editconf
2. solvate the system after step 1 with insane.py to get the final system.
I am facing a little problem in step 2, the script places water at the gaps found in the membrane between two lipids. I know i have to edit the script where the solvent grid is calculated to exclude the lipid cells as well for the above steps to work fine. But I dont know much of pyhton to to this can you let me know if there is a way around this. I tried using genbox but that also dose the same mistake, i know that if i can bundle some of the water molecules together, genbox option will work decently. But if i could make these changes in the script it will work better than genbox.
I am using the insane.py script to build a CG membrane protein system which has 2 bilayers in it. due to the complexity involved I built the system in 2 steps
1. build the membrane around the protein using insane.py without any solvent and assemble the system using editconf
2. solvate the system after step 1 with insane.py to get the final system.
I am facing a little problem in step 2, the script places water at the gaps found in the membrane between two lipids. I know i have to edit the script where the solvent grid is calculated to exclude the lipid cells as well for the above steps to work fine. But I dont know much of pyhton to to this can you let me know if there is a way around this. I tried using genbox but that also dose the same mistake, i know that if i can bundle some of the water molecules together, genbox option will work decently. But if i could make these changes in the script it will work better than genbox.
Please Log in or Create an account to join the conversation.
- tsjerk
-
- Offline
- Expert Boarder
Less
More
- Posts: 103
10 years 3 months ago #3475
by tsjerk
Replied by tsjerk on topic Using insane.py
Have you tried building each membrane separately (with solvent) and then merging the two? The exclusion of solvent from the bilayer is a bit hackish as it is, and it's quite hard to get that done for multiple bilayers. It has to wait for insane2, but we first have to write this one up :)
Please Log in or Create an account to join the conversation.
- Tocci_89
-
- Offline
- Fresh Boarder
Less
More
- Posts: 9
9 years 11 months ago #3810
by Tocci_89
Replied by Tocci_89 on topic Using insane.py
Hi everyone,
I'm new in martini and I'm working whit it to set up GPCR system simulation. I started building a simple POPC membrane bilayer containing my protein using insane.py. All went well: the bilayer has the dimensions and the area per lipid hoped.
Now I'm visualizing the output in VMD and I see that lipids are too much ordinated and so the solvent too. The question is: does insane reach the desired area per lipid simply placing the molecules or does it perform any kind of relaxation-compression cycles to pack the membrane in a more tight way?
If not, how can I get a GPCR-into-bilayer system reliable for a simulation?
Thank you
I'm new in martini and I'm working whit it to set up GPCR system simulation. I started building a simple POPC membrane bilayer containing my protein using insane.py. All went well: the bilayer has the dimensions and the area per lipid hoped.
Now I'm visualizing the output in VMD and I see that lipids are too much ordinated and so the solvent too. The question is: does insane reach the desired area per lipid simply placing the molecules or does it perform any kind of relaxation-compression cycles to pack the membrane in a more tight way?
If not, how can I get a GPCR-into-bilayer system reliable for a simulation?
Thank you
Please Log in or Create an account to join the conversation.
Time to create page: 0.203 seconds