Hello Zhicheng,
Thanks for your reply and suggestions. I will then try to explicitly
specify the donors and acceptors.
All the best,
Qinghua
On 10/10/2018 02:15 AM, Zuo, Zhicheng wrote:
> 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 Wed Oct 10 2018 - 03:00:02 PDT
