Hi,
The distance is calculated between heavy atoms; in the Leu5 to Ala9
case the distance is 3.02, so it just misses the cutoff. Try adding
'dist 3.3' to the hbond command.
-Dan
On Thu, Sep 20, 2012 at 2:19 AM, vaibhav dixit <vaibhavadixit.gmail.com> wrote:
> 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 avgout hbavg_2PRG_PDB.dat
> ----
>
> Output of cpptraj
> ---
> CPPTRAJ: Trajectory Analysis. V12.3
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
>> [bondsearch]
> Info: Bond info will be determined from distance search if not present.
>> [molsearch]
> Info: Molecule info will be determined from bonds if not present.
>> [parm 2PRG_RGZ_VAC.pdb]
> Reading PDB file 2PRG_RGZ_VAC.pdb as topology file.
> 2PRG_RGZ_VAC.pdb: determining bond info from distances.
> 2PRG_RGZ_VAC.pdb: 2263 bonds to hydrogen, 2242 other bonds.
>> [trajin 2PRG_RGZ_VAC.pdb]
> [2PRG_RGZ_VAC.pdb] contains 1 frames.
>> [hbond .C,N,H,O avgout hbavg_2PRG_PDB.dat]
>>
> INPUT TRAJECTORIES:
> [2PRG_RGZ_VAC.pdb] is a PDB file, Parm 0 (reading 1 of 1)
> Coordinate processing will occur on 1 frames.
>
> PARAMETER FILES:
> 0:
> /home/gncp/Documents/MD/PPAR_MD_study/100ns_MD_inputfiles/2PRG_RGZ_VAC.prmtop,
> 4466 atoms, 272 res, no box, 1 frames
> 1: 2PRG_RGZ_VAC.pdb, 4466 atoms, 272 res, no box, 2 mol
>
> REFERENCE COORDS:
> No reference coordinates.
> No frames defined.
>
> OUTPUT TRAJECTORIES:
> No files.
>
> ACTIONS: Initializing 1 actions:
> 0: [hbond .C,N,H,O avgout hbavg.dat]
> HBOND: Searching for Hbond donors/acceptors in region specified by
> .C,N,H,O
> Distance cutoff = 3.000, Angle Cutoff = 135.000
> Dumping Hbond avgs to hbavg_2PRG_PDB.dat
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> PARM [2PRG_RGZ_VAC.prmtop]: Setting up 1 actions.
> 0: [hbond .C,N,H,O avgout hbavg_2PRG_PDB.dat]
> 2PRG_RGZ_VAC.prmtop: Setting up 4506 bonds.
> Set up 542 acceptors:
> Set up 263 donors:
> ----- [2PRG_RGZ_VAC.pdb] (1-1, 1) -----
> 100% Complete.
>
> Read 1 frames and processed 1 frames.
>
> ACTION OUTPUT:
>
> DATASETS:
> There is 1 data set: NumHB_00000
> DATAFILE OUTPUT:
> hbavg_2PRG_PDB.dat: Acceptor,DonorH,Donor,Frames,Frac,AvgDist,AvgAng
>
>
> 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
>
> _______________________________________________
> 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
Received on Thu Sep 20 2012 - 07:30:04 PDT
