Psf file

LAMMPS LAMMPS General Discussion
1

I want to simulate a protein using charmm force field.

I have a pdb file for it. As it is not a known structure, I have built it from MODELLER software. Then I need to create a data file for the charmm force field. Unfortunately the modeller has not given a regular file (the columns 10 and 11 interruption). To build a data file for lammps I need to use this command as you know (perl charmm2lammps.pl all27_prot_lipid configuration_autopsf). But as I mentioned I don’t have a good pdb file so that VMD does not give a psf file (although It is readable via it)
Is there any alternative way?
I have attached the pdb file of the protein.
TvLDH.B99990005.pdb (526.1 KB)

2

You have to either CHARMM or NAMD/psfgen to assign force field types and thus generate the psf file. That is a process that has to happen before LAMMPS gets involved and I strongly recommend to first follow the procedure and test the simulation with CHARMM or NAMD so that you know that they structure is reasonable and you can do meaningful simulations. Based on your previous posts here, you need to take that step very seriously, since that is crucial and you cannot depend on just blindly following some simple commands. You need to understand the entire process.