dear amber users,
i used ptraj for some hydrogen bond analysis, which was provided in the
ptraj tutorial. i could able to continue analysis as the command reaches the
hbond analysis. here i included the output of ptraj. pls provide some
solution for this problems.
one more thing i would like to know that hbond and donor and acceptor
command not found in the manual as well as in the site. but these commands
were used in the ptraj tutorial. i would like to know is any other commands
like this, available to analyse trajectory files or pls update the ptraj
manual.
output of ptraj is
IRIS 6% ptraj ../col.top col.ptraj3.in <
http://col.ptraj3.in>
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...
GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY
PRO HYP GLY PRO HYP GLY PRO PRO GLY PRO
HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP
GLY PRO HYP GLY PRO PRO GLY PRO HYP GLY
PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO
HYP GLY PRO PRO WAT WAT WAT WAT WAT 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.
PTRAJ: Processing input file...
Input is from file col.ptraj3.in <
http://col.ptraj3.in>
PTRAJ: trajin ../col.crd
PTRAJ: trajin ../col.dyn.mdcrd 1 2000 1
PTRAJ: center origin :1-54
Mask [:1-54] represents 654 atoms
PTRAJ: image origin center
Mask [*] represents 3060 atoms
PTRAJ: grid grid.list 8 3.0 8 3.0 24 3.0 :WAT max 0.8
Mask [:WAT] represents 2406 atoms
PTRAJ: donor mask :1-54.O
Mask [:1-54.O] represents 54 atoms
PTRAJ: acceptor WAT O H1
PTRAJ: acceptor WAT O H2
PTRAJ: hbond solventacceptor O H1 solventacceptor O H2 solventneighbor 2
series
hbond
FYI: No output trajectory specified (trajout), none will be saved.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 2001 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (../col.crd) is an AMBER restart file with box information
File (../col.dyn.mdcrd) is an AMBER trajectory (with box info) with 2000
sets
OUTPUT COORDINATE FILE
NULL entry
ACTIONS
1> CENTER to origin via center of geometry, atom selection follows :1-54
7> IMAGE by molecule to origin using the center of mass, atom selection *
(All atoms are selected)
7> GRID at origin will be dumped to filename grid.list as positive density
Atom selection is :55-856
grid points : 8 8 24
grid spacing: 3.000 3.000 3.000
7> HBOND saved to series hbond,
Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information will be dumped for occupancies > 0.00
Estimated memory usage for this hbond call: 1986.48 MB
donors: 54 acceptors: 1604
Processing AMBER restart file ../col.crd
ERROR in safe_malloc: Error in alloc of 693274464 bytes
IRIS 7%
--
S.Sundar Raman
Chemical Lab,
CLRI
Chennai-20
ph: 044-24411830
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Received on Wed Oct 19 2005 - 14:53:00 PDT
