From: Jason Swails (jason.swails_at_gmail.com)
Date: Sun Dec 21 2014 - 20:04:39 CST
On Sun, Dec 21, 2014 at 2:56 PM, Shalton Evans <shalton.evans_at_gmail.com>
> Hello All,
> Does anyone know how to convert an .inpcrd file to a pdb file. I recently
> went through the process of producing .inpcrd and .prmtop files for a
> simulation. I now am not able to use the original .pdb file because atoms
> were added in the process; so there is a difference of atoms between the
> original .pdb file and the newly produced .inpcrd file. I want to use both
> NAMD and VMD so I need to convert this .inpcrd to a .pdb file format. Is
> there a way to do this or a way around this?
VMD reads inpcrd files just fine. inpcrd files have exactly the same
format as "Amber restart files" -- so make sure you use that format when
loading in VMD. From there, you can have VMD save PDB files that you can
use in NAMD when you need a PDB file.
There are also programs in AmberTools that will generate PDB files for you
from a prmtop and inpcrd file, including cpptraj and ambpdb.
-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher
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