Re: [AMBER] can DSSP program give more information

From: vaibhav dixit <vaibhavadixit.gmail.com> Date: Thu, 20 Sep 2012 11:49:24 +0530 · > Ã‚ [bondsearch]

----
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