Hi,
This is dpc.itp file that I downloaded from Dr. Tieleman’s page.
As far as I know, it does not contain dihedrals, bonds, and so on. I have read lots of articles that used this topology but I don’t know how!
I have been working on it for almost two months and I have tried different ways to simulate DPC micelle but nothing happened!
I will appreciate any help.
It certainly does, as any molecule definition would.
These topologies are very old and rely on the ffgmx force field, which was removed from GROMACS years ago for being deprecated and altered in ad hoc ways. The topology you refer to is designed to be used in concert with the micelle coordinates that Peter Tieleman distributes on his website. Getting a functional topology may be somewhat difficult as it requires some force field hacking. You can apply a similar approach to what I outline in KALP-15 in DPPC but you should also consider whether a newer force field would be more suitable altogether (CHARMM36, AMBER Slipids, etc).
Thank you so much Dr. Lemkul.
Now I have another question:
Is it OK to use micelle’s pdb file which has provided in Dr. Teileman’s page and select the values in it for one DPC molecule, in order to create an appropriate pdb file and use ATB server for generating a new topology?
I wouldn’t reinvent the wheel, and you may find that lipid parametrization is quite challenging, even for something “simple” like DPC. Good force fields exist. Either use one of those or be prepared to rigorously parametrize a new one - ATB is quite good but you shouldn’t assume that its models are bulletproof.