AMBER Archive (2006)

Subject: AMBER: ptraj hbond analysis troubles

From: Sayandeep Purkayasth (deepcyan_at_gmail.com)
Date: Wed Oct 04 2006 - 16:14:10 CDT

well i tried doing a hbond analysis as follows:

donor mask :ADE_at_N1
donor mask :THY_at_O4
donor mask :CYT_at_N3,O2
*acceptor mask :THY_at_N3 :THY_at_H3*
acceptor mask :ADE_at_N6 :ADE_at_H62
acceptor mask :ADE_at_N6 :ADE_at_H61
*acceptor mask :GUA_at_N1 :GUA_at_H1*
acceptor mask :GUA_at_N2 :GUA_at_H21
acceptor mask :GUA_at_N2 :GUA_at_H22
acceptor mask :CYT_at_N4 :CYT_at_H41
acceptor mask :CYT_at_N4 :CYT_at_H42
hbond distance 7 series hbond
trajout traj.peptide nobox

the output (only that part showing the error) was as follows:

PTRAJ: acceptor mask :THY_at_N3 :THY_at_H3
Mask [:THY_at_N3] represents *84 atoms*
Mask [:THY_at_H3] represents 18 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :THY_at_N3 and :THY_at_H3 which contain 84 and 18
atoms respectively. Ignoring...

PTRAJ: acceptor mask :GUA_at_N1 :GUA_at_H1
Mask [:GUA_at_N1] represents *84 atoms*
Mask [:GUA_at_H1] represents 24 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :GUA_at_N1 and :GUA_at_H1 which contain 84 and 24
atoms respectively. Ignoring...

can someone please explain where am i going wrong?
for the record, the dna strand under consideration is 42bp long, and has 18
bp AT
for reference, i have attached the .pdb i created from the prmtop and inpcrd
files i used.


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