Hello,
I am running cpptraj to selectively strip atoms from a trajectory;
This is my cpptraj input:
parm mon_d391_holo_nw.parm7
trajin ./mon_d391_holo_nw.crd
center origin
strip :307-318|!(:1-451.CA,:452.C4,.7090,454.N9) parmout mon_d391_holo_n3.parm7 nobox
trajout mon_d391_holo_n3.crd
The goal is to strip residues 307 to 318 and keep all the rest of the CA atoms and individual atoms as marked.
A quick calculation gives: 451-12+3= 442 atoms.
My resulting parm7 has 443 atoms. Examining the parm7 I see an extra atom: (HB in the second row, highlighted in red)
Is something wrong in my syntax? Or is there a bug in cpptraj?
Thanks for your help.
vi mon_d391_holo_n3.parm7
%VERSION VERSION_STAMP = V0001.000 DATE = 10/16/25 20:05:59
%FLAG TITLE
%FORMAT(20a4)
default_name
%FLAG POINTERS
%FORMAT(10I8)
443 4 0 0 0 0 0 0 0 0
443 442 0 0 0 0 0 0 61 0
0 0 0 0 0 0 0 0 2 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
CA CA CA CA CA CA CA CA HB CA CA CA CA CA CA CA CA CA CA CA
CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
CA CA
Roman Osman
Professor
Department of Pharmacological Sciences
Icahn School of Medicine at Mount Sinai
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 16 2025 - 18:00:02 PDT
