Probably not a subject for the amber list but you can use in VMD the file processing sythax in tcl to write out PDBs from the trajectory that contain the 4 pseudoatoms . The command you need is "puts $output [ format "$formatting_rules" "ATOM" "$index" :...]
Greetings
Vlad
On March 13, 2016 6:57:46 PM GMT+01:00, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
>​Thanks Dan for your reply,
>
>I checked the suggested archive:
>http://archive.ambermd.org/201603/0049.html
>
>As your suggestion, indeed currently I am using 4 "vector" commands..
>
>But, in such case, I get four different trajectories, which I visualize
>only after uploading individual trajectory as different "new" molecules
>which is bit cumbersome.
>
>It would be great if I can visualize four center of masses as a
>"single"
>molecule in VMD.
>
>Thanks,
>Hirdesh
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Received on Sun Mar 13 2016 - 11:30:03 PDT
