well i tried doing a hbond analysis as follows:
donor mask :ADE.N1
donor mask :THY.O4
donor mask :CYT.N3,O2
*acceptor mask :THY.N3 :THY.H3*
acceptor mask :ADE.N6 :ADE.H62
acceptor mask :ADE.N6 :ADE.H61
*acceptor mask :GUA.N1 :GUA.H1*
acceptor mask :GUA.N2 :GUA.H21
acceptor mask :GUA.N2 :GUA.H22
acceptor mask :CYT.N4 :CYT.H41
acceptor mask :CYT.N4 :CYT.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.N3 :THY.H3
Mask [:THY.N3] represents *84 atoms*
Mask [:THY.H3] represents 18 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :THY.N3 and :THY.H3 which contain 84 and 18
atoms respectively. Ignoring...
PTRAJ: acceptor mask :GUA.N1 :GUA.H1
Mask [:GUA.N1] represents *84 atoms*
Mask [:GUA.H1] represents 24 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :GUA.N1 and :GUA.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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Received on Sun Oct 08 2006 - 06:07:11 PDT
