Hi,
The 'closest' command will modify your system so that only the solute
and the 10 closest solvent molecules remain. So all you really need is
to add a 'trajout' command at the end to write the coordinates after
'closest', e.g.
trajout closest10.pdb multi
See the manual for all available keywords for 'trajout'.
Also, you can probably replace your center/image commands with
'autoimage'. Hope this helps,
-Dan
On Tue, Mar 28, 2017 at 11:43 PM, 杨满意 <ymy0664.163.com> wrote:
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Mar 30 2017 - 05:30:04 PDT
