[gmx-users] no default bond for the defined 'SPECBOND'

[Li, Tong]

Dear all,

I am developing the top file for a polymer using the force field of 54a7. The 
top files for the head/tail and repeating monomers are well developed and they 
are working fine. The bond between different monomers is defined in 
'sepcbond.dat', however, cannot be recognized as a default bond that has 
pre-defined parameters. Is there a way to modify the 'ffbond.itp' file to 
include the needed information? I used to change it in opls-aa, but cannot do 
it in the 54a7 force field as the force field parameters are defined in a 
different way.

Thanks very much!
Tong
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[gmx-users] how to make molecular model with both ion channel and lipid bilayer?

[Li, Tong]

Dear all,

I am trying to make a model of ion channel with cell membrane. Is there a 
specific software to make this? I mean just the coordination file. VMD can 
generate the membrane automatically, I can find the 'pdb' files of ion 
channels, but I have no idea how to combine them.

Thanks all,
Tong
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