Dear Dr. Daniel and amber users,
It has worked, but there are still some backbone H-bonds missing due to
deviation from the cutoff values.
So the question is to how far should I relax these cutoff values to cover
the largest possible deviation from ideal H-bond in the peptide backbone?
Please let me know if you are aware of any review on this topic.
Thank you.
On Thu, Sep 20, 2012 at 7:47 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>
--
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
Received on Mon Sep 24 2012 - 05:00:03 PDT
