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pdb2gmx with DPPG
- nanogod
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12 years 11 months ago - 12 years 11 months ago #672
by nanogod
pdb2gmx with DPPG was created by nanogod
Hey,
I am trying to convert my cg DPPG lipid bilayer to fg. However, I first need to make the top file for my DPPG lipids. I have a DPPG fg pdb file but pdb2gmx wont create the top file for me! I use the 53A6 force field and it tells me: Atom O13 in residue DPPC 1 not found in rtp entry with 50 atoms.
Well first of all I dont know why it says DPPC :) but I suspect it is the only molecule it can find in the rtp file that resembles DPPG.
Is my problem that there is no DPPG molecule in the rtp file or is it the structure of my DPPG pdb file that is wrong? and how can I then make a top file for my DPPG lipids?
Thanks for the help
best regards
Morten
I am trying to convert my cg DPPG lipid bilayer to fg. However, I first need to make the top file for my DPPG lipids. I have a DPPG fg pdb file but pdb2gmx wont create the top file for me! I use the 53A6 force field and it tells me: Atom O13 in residue DPPC 1 not found in rtp entry with 50 atoms.
Well first of all I dont know why it says DPPC :) but I suspect it is the only molecule it can find in the rtp file that resembles DPPG.
Is my problem that there is no DPPG molecule in the rtp file or is it the structure of my DPPG pdb file that is wrong? and how can I then make a top file for my DPPG lipids?
Thanks for the help
best regards
Morten
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- xavier
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12 years 10 months ago #680
by xavier
Replied by xavier on topic pdb2gmx with DPPG
The problem you are facing here is that there is no atomistic topology for DPPG in the 53A6 force field file ... you would have to define a topology for it. This will require some work as you'd need to check that the topology gives a relative good behavior of the lipids.
XAvier.
XAvier.
nanogod wrote: Hey,
I am trying to convert my cg DPPG lipid bilayer to fg. However, I first need to make the top file for my DPPG lipids. I have a DPPG fg pdb file but pdb2gmx wont create the top file for me! I use the 53A6 force field and it tells me: Atom O13 in residue DPPC 1 not found in rtp entry with 50 atoms.
Well first of all I dont know why it says DPPC :) but I suspect it is the only molecule it can find in the rtp file that resembles DPPG.
Is my problem that there is no DPPG molecule in the rtp file or is it the structure of my DPPG pdb file that is wrong? and how can I then make a top file for my DPPG lipids?
Thanks for the help
best regards
Morten
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