AMBER Archive (2005)

Subject: Re: AMBER: ptraj hbond analysis

From: haixiao jin (jinhx952_at_gmail.com)
Date: Thu Oct 20 2005 - 06:07:30 CDT

you should divide the input files into smaller one, because the number of
water molecule is too many. it exceed the power of computer .

On 10/19/05, S.Sundar Raman <sundar02_at_gmail.com> wrote:
>
> 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_at_O
> Mask [:1-54_at_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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