Hi,
When you use 'acceptormask', you are overriding the automatic search,
so cpptraj literally uses everything specified by the 'acceptormask'
as a hydrogen bond acceptor (see the manual for complete details). If
you want to omit hydrogens use something like ':1-18&!.H='. Hope this
helps,
-Dan
On Wed, Jun 19, 2019 at 2:26 AM 谭畅 <tanc.sioc.ac.cn> wrote:
>
> Hi everyone,
>
> I am a new I have a small doubt regarding hbond analysis. I found that the line of Acceptor include H of some residues in my output file like this, ARG_13.HH11. I don`t know if there are something wrong in my input file or script. Here aremy input file ,parts of script and parts of the output file.Best wishes,Hermione.hb.trajin
> parm ./complex-nowat.parm7
> trajin ../md.crd
> hbond :1-293 out nhb.dat avgout avghb.dat
> hbond donormask :19-293 acceptormask :1-18 out ABnhb.dat avgout ABavghb.dat
> hbond donormask :1-18 acceptormask :19-293 out BAnhb.dat avgout BAavghb.dat
> #cpptraj -i rmwat.trajin
> #cpptraj -i hb.trajin
> #cpptraj -i rmsd.trajin
> cpptraj -i cluster.trajin
>
> #ambpdb -p ../complex.parm7 < ../md-min.rst > md-min-final.pdb
>
>
>
>
> #Acceptor DonorH Donor Frames Frac AvgDist AvgAng
> GLN_17.OE1 ARG_59.HH22 ARG_59.NH2 5943 0.2377 2.8534 162.3994
> GLN_9.OE1 GLU_262.H GLU_262.N 5596 0.2238 2.8560 159.4634
> ARG_13.HH11 VAL_29.HA VAL_29.CA 1152 0.0461 2.8919 145.6224
> GLN_9.HE21 GLU_262.H GLU_262.N 461 0.0184 2.9097 148.4202
> GLN_9.HB3 ILE_261.HB ILE_261.CB 451 0.0180 2.9446 141.1383
> ARG_13.HD3 GLY_260.HA2 GLY_260.CA 221 0.0088 2.9511 148.2537
> ARG_13.HD2 ILE_261.HG23 ILE_261.CG2 169 0.0068 2.9451 141.6353
> LEU_10.HD22 VAL_29.HA VAL_29.CA 144 0.0058 2.9482 140.4503
> NME_18.H PRO_35.HD3 PRO_35.CD 136 0.0054 2.8367 144.7802
> ARG_13.HD2 ILE_261.HG22 ILE_261.CG2 134 0.0054 2.9387 141.9598
> LYS_3.HE2 ASP_22.HB3 ASP_22.CB 133 0.0053 2.8980 145.4082
>
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Received on Wed Jun 19 2019 - 03:30:02 PDT
