Hi,
You can remove all atoms except hydrogens from your system with the
following cpptraj script:
parm <topology file>
trajin <coordinate file>
strip !(.H=)
trajout <output trajectory name>
where <topology file> is your topology file, <coordinate file> is your
trajectory (for a PDB these are the same file), and <output trajectory
name> is your output trajectory. You can write into any format cpptraj
supports - see the manual for details.
-Dan
On Wed, Feb 24, 2016 at 4:52 AM, Madhura De <madhurade.yahoo.co.in> wrote:
> Hello!
> I use Amber14 suite. I am about to do an NMR refinement of a DNA duplex and will be using IRMA (http://www.nmr.chem.uu.nl/Software/irma.php). The input file for IRMA requires only protons to be extracted from all-atom coordinate or trajectory file.Can you tell me the command by which I can extract only the protons from mdcrd or pdb file?
> MadhuraBose InstituteIndia
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Feb 24 2016 - 07:30:05 PST
