Dear Daniel,
Thanks a lot for the tip, it is more convenient. :-)
All the best,
Qinghua
On 10/10/2018 02:23 PM, Daniel Roe wrote:
> Instead of explicit donor and acceptor masks just use :1-169 and the
> ‘nointramol’ keyword. This will let cpptraj choose common hydrogen bonding
> pairs, ignoring intramolecular hydrogen bonds.
>
> -Dan
>
> On Tue, Oct 9, 2018 at 7:04 PM Qinghua Liao <scorpio.liao.gmail.com> wrote:
>
>> 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 - 09:00:03 PDT
