Analyze CHARMM PSF+DCD with CPPTRAJ

I am using CHARMM force field these days. So the corresponding files for MD simulation are PSF and PDB (PRMTOP and INPCRD in AMBER). The problem is that AMBERTOOLS has power tools of CPPTRAJ and parallel version CPPTRAJ.OMP. I used them a lot for commands like hbond, lie, radial or watershell, autoimage, etc. But CPPTRAJ can not deal with PSF very well.

 

The solution is converting PSF to PRMTOP, then use CPPTRAJ for the calculation.

Here, we need parmed.py in AMBERTOOLS.

The input script is below. Run parmed.py < script in the terminal.

chamber -top top_all36_prot.rtf -param par_all36m_prot.prm -str toppar_water_ions.str -psf your.psf -crd your.crd
outparm your.prmtop
quit

 

So you may use the output PRMTOP in CPPTRAJ now. You need to check the PRMTOP to find proper residue names of the script for CPPTRAJ. WAT will be changed to TIP3 (in TIP3P water box).

 

Sometimes, I have to calculate self-diffusion coefficient, so I never wrap box during the simulation. I always use AUTOIMAGE in CPPTRAJ to get the box-shape trajectory. There is one more problem in this case. VMD can not read the PRMTOP got from PSF. We can use PSF instead of PRMTOP, then load DCD file for visualization.

vmd your.psf box-shape.dcd

 

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