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.O15
# specify the ACCEPTOR(s)
acceptor mask :1-5.N6 :1-5.H118
acceptor mask :1-5.N7 :1-5.H129
acceptor mask :1-5.N4 :1-5.H79
acceptor mask :1-5.N5 :1-5.H90
acceptor mask :1-5.N2 :1-5.H40
acceptor mask :1-5.N3 :1-5.H51
acceptor mask :1-5.N :1-5.H
acceptor mask :1-5.N1 :1-5.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.O15
Mask [:1-5.O15] represents 5 atoms
PTRAJ: acceptor mask :1-5.N6 :1-5.H118
Mask [:1-5.N6] represents 5 atoms
Mask [:1-5.H118] represents 5 atoms
PTRAJ: acceptor mask :1-5.N7 :1-5.H129
Mask [:1-5.N7] represents 5 atoms
Mask [:1-5.H129] represents 5 atoms
PTRAJ: acceptor mask :1-5.N4 :1-5.H79
Mask [:1-5.N4] represents 5 atoms
Mask [:1-5.H79] represents 5 atoms
PTRAJ: acceptor mask :1-5.N5 :1-5.H90
Mask [:1-5.N5] represents 5 atoms
Mask [:1-5.H90] represents 5 atoms
PTRAJ: acceptor mask :1-5.N2 :1-5.H40
Mask [:1-5.N2] represents 5 atoms
Mask [:1-5.H40] represents 5 atoms
PTRAJ: acceptor mask :1-5.N3 :1-5.H51
Mask [:1-5.N3] represents 5 atoms
Mask [:1-5.H51] represents 5 atoms
PTRAJ: acceptor mask :1-5.N :1-5.H
Mask [:1-5.N] represents 5 atoms
Mask [:1-5.H] represents 5 atoms
PTRAJ: acceptor mask :1-5.N1 :1-5.H11
Mask [:1-5.N1] represents 5 atoms
Mask [:1-5.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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Received on Sun Dec 03 2006 - 06:07:53 PST
