Dear AMBER users
I have used ptraj to do some hbond analysis of an MD trajectory.
I have some doubts about the results. The %occupied is greater than 1000 in many cases of solvent acceptor and solvent donor when the imaged trajectory is used.
When the original trajectory is used the %occupied is around 700 in many cases.
From the mail archive I understand that it means about 10 / 7 water molecules are hydrogen bonded to the particular atom.
Is it normal?
Which one is the correct method? The output obtained is attached.
My input script is
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# hydrogen bond analysis
# Read in trajectory
trajin ../ade1l_md9.mdcrd
trajin ../ade1l_md10.mdcrd
trajin ../ade1l_md11.mdcrd
trajin ../ade1l_md12.mdcrd
..
..
trajin ../ade1l_md30.mdcrd
center:1-8 mass origin
image origin center
center:1-17 mass origin
image origin center
rms first mass out rms:1-17
prnlev 3
#
# backbone + sugar
#
donor mask .O1P
donor mask .O2P
donor mask .O3'
donor mask .O5'
donor mask .O4'
acceptor mask :8.O3' :8.H3T
acceptot mask :17.O3' :17.H3T
acceptor mask :1.O5' :1.H5T
acceptor mask :9.O5' :9.H5T
#
# minor groove
#
donor RG N3
donor RG5 N3
donor RG3 N3
donor RA N3
donor RC O2
donor RC5 O2
donor RC3 O2
donor RU O2
acceptor RG N2 H22
acceptor RG3 N2 H22
acceptor RG5 N2 H22
#
# major groove
#
donor RG O6
donor RG5 O6
donor RG3 O6
donor RG N7
donor RG3 N7
donor RG5 N7
donor RA N7
acceptor RA N6 H62
donor RU O4
acceptor DC N4 H42
acceptor DC3 N4 H42
prnlev 0
hbond out ade1l_hbond_wat.out \
solventdonor WAT O \
solventacceptor WAT O H1 \
solventacceptor WAT O H2 \
time 1.0 angle -1.0 distance 3.5
==================================================================
Thanks in advance
Mathew
/\/\athew
Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India
email mathew_kvarghese.yahoo.co.in
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Received on Thu Nov 17 2005 - 04:53:00 PST
