Dears
I have a question in CPPTRAJ.
Now I wanted to extract the solute molecule (the first residue) and 10 solvent molecules closect to the solute from the .mdcrd file.
Can I use some commands in Amber to get a .pdb files or other files which contain this 11 molecules' coordinate information.
when I use the cloest command in cpptraj, I can get a .dat file which contain Frame Molecule Distance FirstAtom# information for the 11 molecules and also a new .prmtop
file for the 11 molecules. But I don't know how to convert it to coordinate information contained files
my cpptraj.in:
parm file.prmtop
trajin file.mdcrd 210 600 20
center :1 origin mass
image origin center
solvent :2-880
closest 10 :1 first closestout closet.dat outprefix closest
run
Thanks very much!
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Received on Tue Mar 28 2017 - 21:00:03 PDT
