Dear Dr. Daniel Roe and amber users,
I have tried your suggestion and it has worked to give a list of backbone
Hbonds. But the problem is that it has missed a number of backbone Hbonds
for no apparent reason. For e.g. in the attached PDB file there is a
backbone hbond between LEU5 and ALA9, but it is not appearing in the output
file shown below. This hbond does seem to be within the
cutoff i.e. Distance cutoff = 3.000, Angle Cutoff = 135.000. The distance
and angle values seen in pymol are 2.1 A and angle 149.7 respectively. This
hbond was picked when MD trajectory was used for analysis. GLU1 and ASP4 is
another e.g. of the pair that is missed. Output file for hbond analysis
using MD trajectory is also attached.
Please help me understand this problem and probable solution to the same.
Will changing the cutoff criteria help?
hbavg_2PRG_PDB.dat file is shown below:
--------
#Acceptor DonorH Donor Frames Frac
AvgDist AvgAng
SER_2.O ARG_6.H ARG_6.N 1 1.0000
2.9402 150.6379
ALA_3.O ALA_7.H ALA_7.N 1 1.0000
2.9330 159.3510
ASP_4.O LEU_8.H LEU_8.N 1 1.0000
2.7803 151.1891
ARG_6.O LYS_10.H LYS_10.N 1 1.0000
2.9164 159.6609
ALA_7.O HIE_11.H HIE_11.N 1 1.0000
2.9643 158.9288
LYS_10.O ASP_14.H ASP_14.N 1 1.0000
2.8100 166.2507
LEU_12.O TYR_16.H TYR_16.N 1 1.0000
2.8682 146.3665
TYR_13.O ILE_17.H ILE_17.N 1 1.0000
2.8551 153.6373
SER_15.O SER_19.H SER_19.N 1 1.0000
2.8770 135.4296
THR_23.O ALA_27.H ALA_27.N 1 1.0000
2.8823 166.7609
LYS_24.O ARG_28.H ARG_28.N 1 1.0000
2.7262 169.7005
ALA_27.O LEU_31.H LEU_31.N 1 1.0000
2.9733 170.2207
ALA_29.O THR_32.H THR_32.N 1 1.0000
2.8523 138.4319
ALA_29.O GLY_33.H GLY_33.N 1 1.0000
2.8457 157.0522
GLN_139.O PHE_41.H PHE_41.N 1 1.0000
2.8930 155.6155
PHE_141.O ILE_43.H ILE_43.N 1 1.0000
2.8964 155.8008
ASP_45.O LEU_49.H LEU_49.N 1 1.0000
2.9385 146.5807
MET_46.O MET_50.H MET_50.N 1 1.0000
2.9921 152.3481
ASN_47.O MET_51.H MET_51.N 1 1.0000
2.9145 165.6265
SER_48.O GLY_52.H GLY_52.N 1 1.0000
2.8184 149.3439
LEU_49.O GLU_53.H GLU_53.N 1 1.0000
2.9578 168.1326
MET_50.O ASP_54.H ASP_54.N 1 1.0000
2.8555 146.7454
GLN_65.O GLN_67.H GLN_67.N 1 1.0000
2.9724 144.6076
GLU_70.O ARG_74.H ARG_74.N 1 1.0000
2.9795 149.5296
VAL_71.O ILE_75.H ILE_75.N 1 1.0000
2.9659 178.0256
ILE_73.O GLN_77.H GLN_77.N 1 1.0000
2.8130 162.2505
GLN_77.O PHE_81.H PHE_81.N 1 1.0000
2.9246 154.9579
GLN_80.O VAL_84.H VAL_84.N 1 1.0000
2.9488 144.5826
SER_83.O VAL_87.H VAL_87.N 1 1.0000
2.8084 152.6375
ALA_86.O ILE_90.H ILE_90.N 1 1.0000
2.8602 167.0000
VAL_87.O THR_91.H THR_91.N 1 1.0000
2.8969 148.2197
GLU_89.O TYR_93.H TYR_93.N 1 1.0000
2.9807 160.2325
ILE_90.O ALA_94.H ALA_94.N 1 1.0000
2.7765 158.3892
TYR_93.O SER_96.H SER_96.N 1 1.0000
2.8651 147.0574
PHE_100.O LEU_103.H LEU_103.N 1 1.0000
2.8551 167.3202
ASN_106.O THR_110.H THR_110.N 1 1.0000
2.9623 162.4209
ASP_107.O LEU_111.H LEU_111.N 1 1.0000
2.6953 175.8800
GLN_108.O LEU_112.H LEU_112.N 1 1.0000
2.8832 161.3556
VAL_109.O LYS_113.H LYS_113.N 1 1.0000
2.7630 165.3675
THR_110.O TYR_114.H TYR_114.N 1 1.0000
2.9757 160.4490
LEU_111.O GLY_115.H GLY_115.N 1 1.0000
2.8189 138.1512
LEU_112.O VAL_116.H VAL_116.N 1 1.0000
2.8196 153.1136
VAL_116.O ILE_120.H ILE_120.N 1 1.0000
2.8969 147.7243
HIE_117.O TYR_121.H TYR_121.N 1 1.0000
2.9780 173.9909
ILE_119.O MET_123.H MET_123.N 1 1.0000
2.8926 164.7924
ILE_120.O LEU_124.H LEU_124.N 1 1.0000
2.7780 149.1958
LEU_124.O LEU_127.H LEU_127.N 1 1.0000
2.7625 143.5065
LEU_127.O LEU_134.H LEU_134.N 1 1.0000
2.9101 162.5312
GLY_140.O ILE_135.H ILE_135.N 1 1.0000
2.7536 166.5741
SER_136.O GLN_139.H GLN_139.N 1 1.0000
2.8689 158.1205
ILE_135.O GLY_140.H GLY_140.N 1 1.0000
2.9270 164.7978
PHE_41.O PHE_141.H PHE_141.N 1 1.0000
2.8110 144.8339
VAL_133.O MET_142.H MET_142.N 1 1.0000
2.9499 156.4954
ASP_131.O ARG_144.H ARG_144.N 1 1.0000
2.7912 172.8817
PHE_146.O SER_149.H SER_149.N 1 1.0000
2.8926 154.4458
MET_158.O PHE_162.H PHE_162.N 1 1.0000
2.9883 160.2759
GLU_159.O GLU_163.H GLU_163.N 1 1.0000
2.9544 169.4271
PRO_160.O PHE_164.H PHE_164.N 1 1.0000
2.9859 149.5678
LYS_161.O ALA_165.H ALA_165.N 1 1.0000
2.7639 159.9627
PHE_162.O VAL_166.H VAL_166.N 1 1.0000
2.9050 172.0749
PHE_164.O PHE_168.H PHE_168.N 1 1.0000
2.7533 168.7545
ALA_165.O ASN_169.H ASN_169.N 1 1.0000
2.6425 174.2960
PHE_168.O LEU_171.H LEU_171.N 1 1.0000
2.9658 163.4403
ASN_169.O GLU_172.H GLU_172.N 1 1.0000
2.8775 145.5978
ASP_175.O ALA_179.H ALA_179.N 1 1.0000
2.9434 169.5953
LEU_178.O ILE_182.H ILE_182.N 1 1.0000
2.8422 165.6097
ALA_183.O LEU_187.H LEU_187.N 1 1.0000
2.9997 174.7092
ILE_186.O SER_188.H SER_188.N 1 1.0000
2.8414 146.0835
VAL_197.O GLU_201.H GLU_201.N 1 1.0000
2.9803 160.4312
ILE_200.O GLN_204.H GLN_204.N 1 1.0000
2.9569 165.8416
GLU_201.O ASP_205.H ASP_205.N 1 1.0000
2.8609 154.2235
ILE_203.O LEU_207.H LEU_207.N 1 1.0000
2.9682 168.4089
GLN_204.O LEU_208.H LEU_208.N 1 1.0000
2.6754 159.5915
ASN_206.O ALA_210.H ALA_210.N 1 1.0000
2.9264 166.0306
LEU_207.O LEU_211.H LEU_211.N 1 1.0000
2.8193 149.7536
LEU_208.O GLU_212.H GLU_212.N 1 1.0000
2.8894 166.3256
GLN_209.O LEU_213.H LEU_213.N 1 1.0000
2.9706 167.2493
ALA_210.O GLN_214.H GLN_214.N 1 1.0000
2.9534 155.9650
LEU_211.O LEU_215.H LEU_215.N 1 1.0000
2.8850 167.1147
LEU_213.O LEU_217.H LEU_217.N 1 1.0000
2.9550 168.6973
GLN_214.O ASN_218.H ASN_218.N 1 1.0000
2.8147 163.3070
LEU_225.O LEU_229.H LEU_229.N 1 1.0000
2.8552 158.7442
PHE_226.O LEU_230.H LEU_230.N 1 1.0000
2.9931 166.1041
GLN_231.O THR_234.H THR_234.N 1 1.0000
2.9704 161.5461
LYS_232.O LEU_236.H LEU_236.N 1 1.0000
2.9508 164.1739
THR_234.O GLN_238.H GLN_238.N 1 1.0000
2.9962 157.9781
ASP_235.O ILE_239.H ILE_239.N 1 1.0000
2.8563 159.6231
GLN_238.O GLU_242.H GLU_242.N 1 1.0000
2.8155 163.7126
ILE_239.O HIE_243.H HIE_243.N 1 1.0000
2.9613 169.6937
VAL_240.O VAL_244.H VAL_244.N 1 1.0000
2.9342 156.5157
THR_241.O GLN_245.H GLN_245.N 1 1.0000
2.9680 151.7100
GLU_242.O LEU_246.H LEU_246.N 1 1.0000
2.9302 156.4756
HIE_243.O LEU_247.H LEU_247.N 1 1.0000
2.9615 141.0824
LEU_247.O LYS_251.H LYS_251.N 1 1.0000
2.9949 162.2226
GLN_248.O LYS_252.H LYS_252.N 1 1.0000
2.8151 143.3081
VAL_249.O THR_253.H THR_253.N 1 1.0000
2.9076 145.4303
ILE_250.O GLU_254.H GLU_254.N 1 1.0000
2.8081 153.0514
HIE_260.O GLN_264.H GLN_264.N 1 1.0000
2.7367 137.7615
PRO_261.O GLU_265.H GLU_265.N 1 1.0000
2.8669 151.1518
LEU_263.O TYR_267.H TYR_267.N 1 1.0000
2.8687 171.1373
GLN_264.O LYS_268.H LYS_268.N 1 1.0000
2.8391 140.4709
------
cpptraj command
----
cpptraj -p 2PRG_RGZ_VAC.prmtop < hbond_2PRG_pdb.in
----
cpptraj INPUT file used
---
bondsearch
molsearch
parm 2PRG_RGZ_VAC.pdb
trajin 2PRG_RGZ_VAC.pdb
hbond .C,N,H,O angle 140avgout hbavg_2PRG_PDB.dat
----
On Tue, Sep 18, 2012 at 6:34 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Cpptraj and ptraj can both read PDBs. In order to use the hbond
> command in cpptraj with PDB as parm you need to generate bond/mol info
> (with bondsearch/molsearch keywords) since the PDB doesn't have it
> (this will be done automatically in future releases of cpptraj). E.g.,
>
> bondsearch
> molsearch
> parm input.pdb
> trajin input.pdb
> hbond .C,N,H,O avgout hbavg.dat
>
> Ptraj doesn't need bond/mol info, but you need to manually specify
> hbonding atoms with donor/acceptor keywords prior to the hbond
> command. See the manual for more details.
>
> Hope this was helpful,
>
> -Dan
>
> On Mon, Sep 17, 2012 at 11:41 PM, vaibhav dixit <vaibhavadixit.gmail.com>
> wrote:
> > Can we do this with a pdb file? i.e. generate a list of pair of residue
> > names/IDs between which there are backbone H-bond?
> > Thanks for your suggestions.
> >
> > On Mon, Sep 17, 2012 at 6:08 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> Why not just use the hbond command? In cpptraj something like 'hbond
> >> .C,N,H,O avgout hbavg.dat' should work.
> >>
> >> -Dan
> >>
> >> On Monday, September 17, 2012, vaibhav dixit wrote:
> >>
> >> > Dear Amber users,
> >> > I'm using secstruct command for making secondary structure prediction.
> >> > Manual says that it uses DSSP program. My question is...
> >> > Can DSSP program be used to print a list of pair of AA residue
> names/IDs
> >> > that form backbone H-bonds in a given protein sequence?
> >> > It does seem to calculate/use this information for giving the usual
> >> output
> >> > files.
> >> >
> >> > Thanks for your help and suggestions in advance.
> >> >
> >> > --
> >> > With regards
> >> >
> >> > Vaibhav A. Dixit
> >> > Ph.D. Scholar
> >> > Department of Medicinal Chemistry
> >> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> >> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> >> > Punjab -160 062 INDIA
> >> > Phone (Mobile): +919915214408
> >> > E-mail: vaibhavadixit.gmail.com <javascript:;>
> >> > www.niper.nic.in
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org <javascript:;>
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 201
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-9119 (Fax)
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D. Scholar
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Wed Sep 19 2012 - 23:30:02 PDT
