I will build my dgdg bilayer from scratch in Pymol builder. I will use OPLS-AA force field. I checked other bilayers and I see that lipids in some bilayers there is no hydrogens. Why?
For example here:
http://people.ucalgary.ca/~tieleman/download.html
In this case, the PDB files are similar to PDB files of X-ray structures downloaded from the Protein Data Bank. These typically do not include hydrogens, which are not resolved at the X-ray or synchrotron radiation wavelengths used. You need to add hydrogens using appropriate software.
It depends on the force-field used in the original MD simulations. There are all-atom force-fields like for example Berger lipids where the hydrogen atoms are missing. Their influence is encountered parametically at the heavy atoms.
This PDB files database does not say where the structures are from. What are the original force-fields they were built in. So it is of no use I would say.
The parameters and the atom names given in PDB have to correspond to those given in force-field description if you want to run a simulation with them. Just prepare your fresh bilayers. It would be better.
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