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genareting more peptides/molecules in a lipdi bilayer
- Newguy
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5 years 9 months ago #7746
by Newguy
genareting more peptides/molecules in a lipdi bilayer was created by Newguy
Moin everybody,
firstly thank you for this amazing way to simulate (simulating itself is for me way more fun like this. I am kind of new in this genre....).
My question is, if there is a way to tell insane to insert more peptides than one in a bilayer or do I need to merge the pdb files before?
Thank you for your answer :D
PS: Nice tutorials. Way more understandable (doesn't just leave the brain) than everything I read before.
PPS: Is there a tut for DAFT?
firstly thank you for this amazing way to simulate (simulating itself is for me way more fun like this. I am kind of new in this genre....).
My question is, if there is a way to tell insane to insert more peptides than one in a bilayer or do I need to merge the pdb files before?
Thank you for your answer :D
PS: Nice tutorials. Way more understandable (doesn't just leave the brain) than everything I read before.
PPS: Is there a tut for DAFT?
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- riccardo
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5 years 8 months ago #7752
by riccardo
Replied by riccardo on topic genareting more peptides/molecules in a lipdi bilayer
Hi Newguy,
you're welcome ;)
I am not an insane expert, but merging the pdb file sounds like a nice workaround. An alternative would be to prepare two separate simulation boxes with insane - with one protein each - and then merge them afterwards (say, you make one box with size 10x5x10, the other one with size 10x5x10 and the final box will be 10x10x10). You can extend this to multiple proteins.
Regarding DAFT, I am not aware of any tutorial on this website, nor I know of any other tutorial available somewhere else, sorry (googling, which I guess you had tried, also did not help).
you're welcome ;)
I am not an insane expert, but merging the pdb file sounds like a nice workaround. An alternative would be to prepare two separate simulation boxes with insane - with one protein each - and then merge them afterwards (say, you make one box with size 10x5x10, the other one with size 10x5x10 and the final box will be 10x10x10). You can extend this to multiple proteins.
Regarding DAFT, I am not aware of any tutorial on this website, nor I know of any other tutorial available somewhere else, sorry (googling, which I guess you had tried, also did not help).
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- Newguy
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5 years 8 months ago #7757
by Newguy
Replied by Newguy on topic genareting more peptides/molecules in a lipdi bilayer
thanks riccardo (will try that to get exact locations) :D
Found also a way (which is totally random but it worked)
1. martinize the peptid
2. gmx insert the pepitd as much as you want
PS: dont martinize after gmx insert. Didn't work with me
3. update the .top file with the matching amount peptids (will always say 1 and if you don't change it gromacs gets realy confused (thinks all your peptids are one big one))
4. use insane.py (don't understand at the moment the pattern where the bilayer is placed with insane but "$ยง" it)
(lipids maybe just in the middle of the box)
5. update .top (again says just 1)
PS: use the same boxsize
After that there is just the normal process needed (minimi, equilibri, dynami)
(big victory shout after that worked)
Found also a way (which is totally random but it worked)
1. martinize the peptid
2. gmx insert the pepitd as much as you want
PS: dont martinize after gmx insert. Didn't work with me
3. update the .top file with the matching amount peptids (will always say 1 and if you don't change it gromacs gets realy confused (thinks all your peptids are one big one))
4. use insane.py (don't understand at the moment the pattern where the bilayer is placed with insane but "$ยง" it)
(lipids maybe just in the middle of the box)
5. update .top (again says just 1)
PS: use the same boxsize
After that there is just the normal process needed (minimi, equilibri, dynami)
(big victory shout after that worked)
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- Pim
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