> On Nov 23, 2014, at 7:27 PM, LI An-Bang <anbangli.qq.com> wrote:
>
> Hi all,
>
>
> I had generated the PRMTOP and INPCRD files of a protein-protein complex structure. And now I want to seperate the two proteins from the PRMTOP and INPCRD files, i.e. to generate PRMTOP and INPCRD files for the two proteins from the files of the complex. How can I do that?
You can use cpptraj or ParmEd to strip out a portion of the system and write another prmtop file. Let’s suppose that your prmtop file is called “combined.parm7” with inpcrd file “combined.rst7" and you want to create a “system1.parm7” and “system2.parm7” file that contains the two subsystems with corresponding inpcrd files. Let’s also assume that subsystem one is 50 residues and subsystem 2 is 40 residues (so you have 90 residues total).
The following ParmEd script will do what you want:
---
parm combined.parm7
parm copy 0
loadRestrt combined.rst7 parm 0
loadRestrt combined.rst7 parm 1
strip :51-90 parm 0
strip :1-50 parm 1
outparm system1.parm7 system1.rst7 parm 0
outparm system2.parm7 system2.rst7 parm 1
---
Assuming this file is called parmed.in, run the command
parmed.py -i parmed.in
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Nov 23 2014 - 18:00:04 PST
