AMBER Archive (2006)

Subject: AMBER: H-bond analysis (Ptraj) input file

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Fri Dec 01 2006 - 10:22:44 CST

Dear All,
 
 I am trying to get information about H-bond in the system. When I use Ptraj to calculate, I found something that I don't understand.
 1. For the acceptor, if I use mask, do I need to specify the heavy atom except the H atom?
 2. How to get a output file with all the H-bond information in it? I tried several time, but always failed.
 
 Does anybody help me figure it out? Thanks a lot!
 
 Here is the input file:
 # calculate the H-Bond
 
 trajin md.mdcrd
 
 # specify the electron pair DONOR
 donor mask :1-5_at_O15
 
 # specify the ACCEPTOR(s)
 
 acceptor mask :1-5_at_N6 :1-5_at_H118
 acceptor mask :1-5_at_N7 :1-5_at_H129
 
 acceptor mask :1-5_at_N4 :1-5_at_H79
 acceptor mask :1-5_at_N5 :1-5_at_H90
 
 acceptor mask :1-5_at_N2 :1-5_at_H40
 acceptor mask :1-5_at_N3 :1-5_at_H51
 
 acceptor mask :1-5_at_N :1-5_at_H
 acceptor mask :1-5_at_N1 :1-5_at_H11
 
 donor print
 acceptor print
 
 hbond print 0.05 out output_hbond2.dat
 go
 
 
 When run it, on the screen, it shows:
 
 Amber8 Module: ptraj
 
 Read in control variables
 Read in atom names...
 Read in charges...
 Read in masses...
 Read in IAC (atoms involved in L-J)...
 Read in NUMEX (index to excl atom list)...
 Read in NNO (index for nonbond of @type)...
 Read in residue labels...
  MIC MIC MIC MIC MIC Na+ Na+ Na+ Na+ Na+
  Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+
  Na+ Na+ Na+ Na+ Na+ WAT WAT WAT WAT WAT
  WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
  ...
  WAT WAT
 Read in the residue to atom pointer list...
 Read in bond parameters RK and REQ...
 Read in angle parameters TK and TEQ...
 Read in dihedral parameters PK, PN and PHASE...
 Read in SOLTY...
 Read in L-J parameters CN1 and CN2...
 Read in info for bonds w/ hydrogen...
 Read in info for bonds w/out hydrogen...
 Read in info for angles w/ hydrogen...
 Read in info for angles w/out hydrogen...
 Read in info for dihedrals w/ hydrogen...
 Read in info for dihedrals w/out hydrogen...
 Read in excluded atom list...
 Read in h-bond parameters: AG, BG, and HBCUT...
 Read in atomic symbols (types)...
 Read in tree information...
 Read in the JOIN info...
 Read in the IROTAT info...
 Scanning Box
 Read in box information...
 Successfully completed readParm.
 
 Initializing state: detected PBC beta angle in prmtop that is not 90.0!
 Assuming this box is a truncated octahedron, angle is 109.471221
 
 PTRAJ: Processing input file...
        Input is from standard input
 
 PTRAJ: trajin LV2nd_1ns_reimage.mdcrd
 Checking coordinates: LV2nd_1ns_reimage.mdcrd
 
 PTRAJ: donor mask :1-5_at_O15
 Mask [:1-5_at_O15] represents 5 atoms
 
 PTRAJ: acceptor mask :1-5_at_N6 :1-5_at_H118
 Mask [:1-5_at_N6] represents 5 atoms
 Mask [:1-5_at_H118] represents 5 atoms
 
 PTRAJ: acceptor mask :1-5_at_N7 :1-5_at_H129
 Mask [:1-5_at_N7] represents 5 atoms
 Mask [:1-5_at_H129] represents 5 atoms
 
 PTRAJ: acceptor mask :1-5_at_N4 :1-5_at_H79
 Mask [:1-5_at_N4] represents 5 atoms
 Mask [:1-5_at_H79] represents 5 atoms
 
 PTRAJ: acceptor mask :1-5_at_N5 :1-5_at_H90
 Mask [:1-5_at_N5] represents 5 atoms
 Mask [:1-5_at_H90] represents 5 atoms
 
 PTRAJ: acceptor mask :1-5_at_N2 :1-5_at_H40
 Mask [:1-5_at_N2] represents 5 atoms
 Mask [:1-5_at_H40] represents 5 atoms
 
 PTRAJ: acceptor mask :1-5_at_N3 :1-5_at_H51
 Mask [:1-5_at_N3] represents 5 atoms
 Mask [:1-5_at_H51] represents 5 atoms
 
 PTRAJ: acceptor mask :1-5_at_N :1-5_at_H
 Mask [:1-5_at_N] represents 5 atoms
 Mask [:1-5_at_H] represents 5 atoms
 
 PTRAJ: acceptor mask :1-5_at_N1 :1-5_at_H11
 Mask [:1-5_at_N1] represents 5 atoms
 Mask [:1-5_at_H11] represents 5 atoms
 
 PTRAJ: donor print
     Atom# Residue# Name -- Atom# Residue# Name
     232 1 O15
     500 2 O15
     768 3 O15
    1036 4 O15
    1304 5 O15
 
 PTRAJ: acceptor print
     Atom# Residue# Name -- Atom# Residue# Name
      16 1 N1 -- 17 1 H11
      35 1 N -- 36 1 H
      81 1 N2 -- 116 1 H40
      85 1 N3 -- 101 1 H51
     148 1 N4 -- 183 1 H79
     152 1 N5 -- 168 1 H90
     233 1 N6 -- 234 1 H118
     252 1 N7 -- 253 1 H129
     284 2 N1 -- 285 2 H11
     303 2 N -- 304 2 H
     349 2 N2 -- 384 2 H40
     353 2 N3 -- 369 2 H51
     416 2 N4 -- 451 2 H79
     420 2 N5 -- 436 2 H90
     501 2 N6 -- 502 2 H118
     520 2 N7 -- 521 2 H129
     552 3 N1 -- 553 3 H11
     571 3 N -- 572 3 H
     617 3 N2 -- 652 3 H40
     621 3 N3 -- 637 3 H51
     684 3 N4 -- 719 3 H79
     688 3 N5 -- 704 3 H90
     769 3 N6 -- 770 3 H118
     788 3 N7 -- 789 3 H129
     820 4 N1 -- 821 4 H11
     839 4 N -- 840 4 H
     885 4 N2 -- 920 4 H40
     889 4 N3 -- 905 4 H51
     952 4 N4 -- 987 4 H79
     956 4 N5 -- 972 4 H90
    1037 4 N6 -- 1038 4 H118
    1056 4 N7 -- 1057 4 H129
    1088 5 N1 -- 1089 5 H11
    1107 5 N -- 1108 5 H
    1153 5 N2 -- 1188 5 H40
    1157 5 N3 -- 1173 5 H51
    1220 5 N4 -- 1255 5 H79
    1224 5 N5 -- 1240 5 H90
    1305 5 N6 -- 1306 5 H118
    1324 5 N7 -- 1325 5 H129
 
 PTRAJ: hbond print 0.05 out output_hbond2.dat
 FYI: No output trajectory specified (trajout), none will be saved.
 
 PTRAJ: Successfully read the input file.
        Coordinate processing will occur on 4690 frames.
        Summary of I/O and actions follows:
 
 INPUT COORDINATE FILES
   File (md.mdcrd) is an AMBER trajectory (with box info) with 4690 sets
 
 OUTPUT COORDINATE FILE
   NULL entry
 
 ACTIONS
   1> HBOND output to file output_hbond2.dat,
       data will be sorted, intra-residue interactions will NOT be included,
       Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
       Hydrogen bond information will be dumped for occupancies > 0.05
       Estimated memory usage for this hbond call: 0.00 MB
       donors: 5 acceptors: 40
 
 
 
 Processing AMBER trajectory file LV2nd_1ns_reimage.mdcrd
 
 Set 1 .................................................
 ...............................
 

Esther B.

 
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