Hi Qinghua:
Yes! I think it would work for you if you explicitly specify the donor and acceptor atoms, something like:
:1-168.O,N,OH,ND,OD1,OD2,OE1,OE2,... (other residual O and N atoms)
:169.O?,N?,... (other polar atoms potentially acting as H-bond donor or acceptor).
In this way, you can safely filter out any unexpected "non-polar" H-bonds returned from cpptraj hbond.
However, for you case, I would recommend the tool "measure hbond" in VMD.
Zhicheng
________________________________
From: Qinghua Liao <scorpio.liao.gmail.com>
Sent: Tuesday, October 9, 2018 4:03:44 PM
To: AMBER Mailing List
Subject: [AMBER] hydrogen bond analysis
Hello,
I am doing hydrogen bond analysis with cpptraj, and I found that
there are some "non hydrogen bonds" which are also accounted as hydrogen
bonds.
I want to calculate the number of hydrogen bond between two groups, and
the commands are:
hbond donormask :1-168 acceptormask :169 out nhb1.dat avgout avghb1.dat
hbond donormask :169 acceptormask :1-168 out nhb2.dat avgout avghb2.dat
Then, in avghb1.dat and avghb2.dat, I found something like this:
GTP_169.O4' LYS_120.HE2 LYS_120.CE 40 0.0001
2.9740 139.9554
GTP_169.H21 LEU_151.HD21 LEU_151.CD2 37 0.0001
2.9313 140.6202
GTP_169.O3G ARG_67.HE ARG_67.NE 36 0.0001
2.9161 148.2551
GTP_169.O3G SER_15.HA SER_15.CA 35 0.0001
2.9812 137.7251
GTP_169.H21 LEU_151.HD23 LEU_151.CD2 33 0.0001
2.9552 142.8424
GTP_169.H21 LEU_151.HD22 LEU_151.CD2 32 0.0001
2.9457 141.9787
GTP_169.H3' ASN_21.HD21 ASN_21.ND2 29 0.0001
2.8299 139.1164
GTP_169.H2'1 LEU_33.HD12 LEU_33.CD1 29 0.0001
2.9602 150.6115
GTP_169.H2'1 LEU_33.HD13 LEU_33.CD1 27 0.0001
2.9721 151.9962
LEU_33.HA GTP_169.H2'1 GTP_169.C2' 1774 0.0059
2.9269 140.0343
ASN_21.HD22 GTP_169.H8 GTP_169.C8 1643 0.0055
2.9193 142.1370
SER_35.HB3 GTP_169.H5'2 GTP_169.C5' 1584 0.0053
2.9213 140.3631
SER_35.HB2 GTP_169.H5'2 GTP_169.C5' 1487 0.0050
2.9192 142.6323
SER_35.HB2 GTP_169.H3' GTP_169.C3' 1379 0.0046
2.9355 144.6187
ASN_21.HD21 GTP_169.H2'1 GTP_169.C2' 666 0.0022
2.9394 144.4345
ASN_21.HD22 GTP_169.H3' GTP_169.C3' 585 0.0019
2.9392 153.2719
How can I avoid to count those "non hydrogen bond", do I have to
explicitly specify the donor and acceptor masks? Thanks a lot!
All the best,
Qinghua
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Received on Tue Oct 09 2018 - 17:30:03 PDT
