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Re: Changing the DSPC lipid to DLPC.
- jhosamelly
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10 years 1 month ago - 10 years 1 month ago #3566
by jhosamelly
Re: Changing the DSPC lipid to DLPC. was created by jhosamelly
I successfully finished the bilayer tutorial.
It says there that we can change the lipid by just changing the name to, say, DOPC at the .top and .mdp files.
I successfully did that as well.
However, I want to make every PC lipid.
DPPC, DLPC, DMPC... etc.
How can I do this? I was not able to change the DSPC bilayer to DLPC because on the no. of beads, correct?
I also want to have .gro files for those lipids as well. Single lipids, not the bilayers. Please help. THANKS.
It says there that we can change the lipid by just changing the name to, say, DOPC at the .top and .mdp files.
I successfully did that as well.
However, I want to make every PC lipid.
DPPC, DLPC, DMPC... etc.
How can I do this? I was not able to change the DSPC bilayer to DLPC because on the no. of beads, correct?
I also want to have .gro files for those lipids as well. Single lipids, not the bilayers. Please help. THANKS.
Last edit: 10 years 1 month ago by jhosamelly.
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- Clement
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10 years 1 month ago #3570
by Clement
Replied by Clement on topic Re: Changing the DSPC lipid to DLPC.
Download the insane script (yes, that's the name of the script) available at this page:
md.chem.rug.nl/cgmartini/index.php/tools2/proteins-and-bilayers
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- jhosamelly
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10 years 1 month ago #3571
by jhosamelly
Replied by jhosamelly on topic Re: Changing the DSPC lipid to DLPC.
Thanks!!! I'll try it later. :))
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- jhosamelly
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10 years 1 month ago #3581
by jhosamelly
Replied by jhosamelly on topic Re: Changing the DSPC lipid to DLPC.
I've been trying to use the insane.py python script to generate a .gro file for a single DLPC. I get an output but I don't think I have the right structure. :(
This is the input command I used.
python insane.py -d 1 -x 1 -y 1 -z 3 -l DLPC -asym 1 -sol 0 -o dlpc.gro
Any help would be greatly appreciated.
This is the input command I used.
python insane.py -d 1 -x 1 -y 1 -z 3 -l DLPC -asym 1 -sol 0 -o dlpc.gro
Any help would be greatly appreciated.
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- helgi
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10 years 1 month ago #3582
by helgi
Replied by helgi on topic Re: Changing the DSPC lipid to DLPC.
Hello, hello,
Here you have to be more specific - why is this not the right structure?
I tried running the same and it appears to work find, here you have to be careful though as insane does not generate "correct" structures. Insane places scaffolds (right beads in mostly the right positions) then when you run EM and equilibrium MD (short time step) the scaffolds adopt the correct structure as defined by the force field.
Hope this helps,
Cheers,
- Helgi
Here you have to be more specific - why is this not the right structure?
I tried running the same and it appears to work find, here you have to be careful though as insane does not generate "correct" structures. Insane places scaffolds (right beads in mostly the right positions) then when you run EM and equilibrium MD (short time step) the scaffolds adopt the correct structure as defined by the force field.
Hope this helps,
Cheers,
- Helgi
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- Clement
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10 years 1 month ago - 10 years 1 month ago #3583
by Clement
Replied by Clement on topic Re: Changing the DSPC lipid to DLPC.
You're generating here a rectangular box of 1x1x3 nm... And you're asking for asymmetry but provide only one type of lipid.
But anyway, doesn't matter. If you want only ONE lipid, create whatever bilayer with python insane.py -box 5,5,5 -l DLPC -o dlpc.gro, and edit to .gro file by deleting everything but the first lipid.
Check the topology of Martini lipids; they're rather simple, +/-1 tail bead at a time. In practice, you can create any lipid (tail and/or head group) from DSPC. As Helgi mentioned above, Martini is flexible enough to allow on-the-fly switching between lipid types.
But anyway, doesn't matter. If you want only ONE lipid, create whatever bilayer with python insane.py -box 5,5,5 -l DLPC -o dlpc.gro, and edit to .gro file by deleting everything but the first lipid.
Check the topology of Martini lipids; they're rather simple, +/-1 tail bead at a time. In practice, you can create any lipid (tail and/or head group) from DSPC. As Helgi mentioned above, Martini is flexible enough to allow on-the-fly switching between lipid types.
Last edit: 10 years 1 month ago by Clement.
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- amiri
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9 years 5 months ago #4172
by amiri
Replied by amiri on topic Re: Changing the DSPC lipid to DLPC.
How can i get to a DPPC_single.gro file?
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9 years 5 months ago #4174
by Clement
Replied by Clement on topic Re: Changing the DSPC lipid to DLPC.
md.chem.rug.nl/cgmartini/images/applicat...bichol/dppc_chol.gro
Open that with a text editor, extract the first residue (first 12 atoms). Don't forget to change the number of atoms (second line of your .gro file), and maybe the box size with editconf.
Open that with a text editor, extract the first residue (first 12 atoms). Don't forget to change the number of atoms (second line of your .gro file), and maybe the box size with editconf.
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9 years 5 months ago #4177
by amiri
Replied by amiri on topic Re: Changing the DSPC lipid to DLPC.
I want to simulate a molecule in DPPC bilayer, I used "editconf" command for set the DPPC and molecule, but i gave an error. My command were respectively:
1)genbox -ci dppc_single.gro -nmol 128 -box 6.9 6.9 6.9 -try 500 -o dppc_128.gro
2) editconf -f molecule.gro -o molecule_newbox.gro -box 6.9 6.9 6.9 -c
3)cat molecule_newbox.gro dppc_128.gro > system.gro
4)grompp -f em.mdp -c system.gro -p dppc.top -maxwarn 10
and gave this error:
atomtype OA not found
I obtained "itp and gro" files of my molecule from ATB ( compbio.biosci.uq.edu.au/atb/ ) and included these files in dppc.top file but i gave above error, what must i do?
Regards,
1)genbox -ci dppc_single.gro -nmol 128 -box 6.9 6.9 6.9 -try 500 -o dppc_128.gro
2) editconf -f molecule.gro -o molecule_newbox.gro -box 6.9 6.9 6.9 -c
3)cat molecule_newbox.gro dppc_128.gro > system.gro
4)grompp -f em.mdp -c system.gro -p dppc.top -maxwarn 10
and gave this error:
atomtype OA not found
I obtained "itp and gro" files of my molecule from ATB ( compbio.biosci.uq.edu.au/atb/ ) and included these files in dppc.top file but i gave above error, what must i do?
Regards,
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- Clement
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9 years 5 months ago - 9 years 5 months ago #4178
by Clement
Replied by Clement on topic Re: Changing the DSPC lipid to DLPC.
Mmmmh... If I'm guessing right, you're trying to mix up coarse-grained structure (that I pointed you to) and topologies with atomistic ones (atom type OA is not a standard Martini bead name).
Here is a forum about the Martini coarse-grained force field, and we try to help people having Martini-related problem. I think yours are more about how to run a simulation with GROMACS, associated file formats, force fields, ...
Define exactly what you want to do, and we could point to the right place for you to start with. Which, from what I gather, isn't here I'm afraid...
Here is a forum about the Martini coarse-grained force field, and we try to help people having Martini-related problem. I think yours are more about how to run a simulation with GROMACS, associated file formats, force fields, ...
Define exactly what you want to do, and we could point to the right place for you to start with. Which, from what I gather, isn't here I'm afraid...
Last edit: 9 years 5 months ago by Clement.
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