As Axel pointed out PDB files lack a lot of information. This missing information means that any tool which converts PDB files needs to make a large number of strong assumptions about your system. Both moltemplate and topotools are general programs and they make few assumptions. So you will have to supply all this information yourself (missing hydrogen atoms, atom types, force field choice, bond ambiguity, etc... There are conflicting several atom naming conventions which make interpreting PDB files somewhat hellish. They require a lot of processing.)
One of these assumptions is the force field you are using. Different PDB conversion tools often only work with one type of force field... So, generally speaking, you need to decide the force field you want to use first, and then choose which simulation software and conversion tool bests supports that force field. If you have decided you want to limit yourself to LAMMPS, then I have heard that charmm2lmp (ch2lamp?) can completely convert PDB files into LAMMPS data files without any other tools needed, but you are limited to using the CHARMM force field (and probably not the latest one. The same could be said about AmberTools+amb2lmp (or amner2lmp?) and Materials studio+msi2lmp. These tools are not fully supported and have their share of bugs. Axel (and Bruce Allen?) have been valiantly attempting to maintain msi2lmp, but it has some limitations that can not be easily addressed. Another alternative is to use the ATB database (see below).
--- recommendation ---
If you are simulating large biomolecules and are willing to start from scratch, then (my impression) is that the most modern and versatile free simulation tool for simulating all-atom proteins, nucleic acids and lipids might be OpenMM.
NAMD, GROMACS, and AMBER and MaterialsStudio are also still very popular and powerful. LAMMPS has some features that none of these programs have, but if you don't need them, then why suffer. All of these simulation programs come with PDB conversion tools which are much more convenient than anything available for LAMMPS (and I hate to say, more likely to be bug free).
--- moltemplate ----
If you wanted to prepare an all-atom simulation of DPPC lipids in moltemplate, it is possible. Its not that difficult. You just have to define a "DPPC" molecule listing all the atom types and bonds explicitly (similar to the "spcl.lt
" file in the moltemplate examples) in that type of lipid. For an example of the file format, see:
You can find all of the atom types you need in the "oplsaa.lt
" file, but you have to choose them carefully.
Alternatively, you generate a "dppc.lt
" file containing DPPC lipid molecule in moltemplate format using the "ATB" database. This is probably the easiest (and safest) way to create these files right now.
(All files are available in moltemplate format, apparently. When I tried it, the process seemed relatively straightforward.)
Once you have defined a "DPPC" molecule in moltemplate, it's not difficult to create a "system.lt
" file which tells moltemplate to generate many copies of these lipid molecules, as well as many water molecules and ions that would be present. You can either use moltemplate ".move()" commands, or PACKMOL (or LipidWrap?) To generate initial coordinates for all the molecules in the simulation which moltemplate can read.
However, if you plan to run all-atom simulations of -proteins-, then it is more difficult. You would have to write definitions for all 20 amino acids, and then create a polymer object linking them together.) I don't run these kinds of simulations, so I never took the time to write these 20 molecule objets, but it should not be -that- difficult. See post here:
For this reason and others, moltemplate is not yet a convenient tool for preparing all-atom simulations of proteins. I don't know if it ever will be. It was intended for coarse grained modeling.
People can spend months figuring out how to convert PDB files I to working simulation input files. (This is not a good file format. I wish it would die. But people keep using it.) This is not easy. It's really time consuming.
I hope this helps give you an idea about the software which is available and their relatively strengths.
PS. I wish I could say more about topotools. I know you can do all this using topotools, but you will need to supply all of these missing details as well.