AMBER Archive (2004)

Subject: AMBER: H bond calculation of CHARMM trajactory using PTRAJ

From: anshul_at_imtech.res.in
Date: Fri Oct 15 2004 - 23:59:33 CDT

Dear amber users,

I am trying to use ptraj for analysis of trajactories given by CHARMM
runs. I calculated the distance between hydrogen bond donor and acceptors
but gives the results of about 8-10 A. I measured the same distances in
insight and found it to be about 3 A.
My system is a small peptide in right handed helical conformation so I try
to get bonds between n and n+4 residue. The input used is as follows:

--------------------------------------------------------------------------
trajin ala.pdb
distance distance1 :2_at_O :6_at_N out dist-init1
distance distance2 :3_at_O :7_at_N out dist-init2
distance distance3 :4_at_O :8_at_N out dist-init3
distance distance4 :5_at_O :9_at_N out dist-init4
distance distance5 :6_at_O :10_at_N out dist-init5
distance distance6 :7_at_O :11_at_N out dist-init6
--------------------------------------------------------------------------

The command used is :
ptraj ala_3.psf < hbdist.in

if I run the same system with trajactories given by amber I get the right
answer. I think there is some problem with the trajin file; but I was not
able to run it with anyother file accept for the pdb file which I
converted from the CHARMM .crd file.

Next I also tried to calculated the H Bonding pattern of the same system,
but I dont get any results in the output. The input used is as follows:

-------------------------------------------------------------------------
trajin ala.pdb
acceptor ALA N N
Donor ALA O
hbond
-------------------------------------------------------------------------

The out put is as follows;

Reading in CHARMM PSF file
Reading in thetitle...
* Insight II-generated PSF for ALA using the charmm27.cfrc forcefield
* Produced on Wed Sep 29 23:26:13 2004 by anshul

Total number is atoms is 112
Reading in the atom information...
Dumping out residue names:
 ACE ALA ALA ALA ALA ALA ALA ALA ALA ALA
 ALA ALA
Dumping state information...
  atoms: 112
  residues: 12
  box length: 0.000 0.000 0.000
  box angles: 90.000 90.000 90.000
  molecules: 1
  max frames: 0

PTRAJ: Processing input file...
       Input is from standard input
PTRAJ: trajin ala.pdb
PTRAJ: acceptor ALA N N
PTRAJ: Donor ALA O
PTRAJ: hbond distance 10
FYI: No output trajectory specified (trajout), none will be saved.
PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 1 frames.
       Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (ala.pdb) is a PDB file
OUTPUT COORDINATE FILE
  NULL entry
ACTIONS
  1> HBOND
      data will be sorted, intra-residue interactions will NOT be
included,
      Distance cutoff is 10.00 angstroms, angle cutoff is 120.00 degrees
      Hydrogen bond information will be dumped for occupancies > 0.00
      Estimated memory usage for this hbond call: 0.00 MB
      donors: 10 acceptors: 11

Processing PDB file ala.pdb

Set 1 .

PTRAJ: Successfully read in 1 sets and processed 1 sets.
       Dumping accumulated results (if any)
  HBOND SUMMARY:
      data was sorted, intra-residue interactions are NOT included,
      Distance cutoff is 10.00 angstroms, angle cutoff is 120.00 degrees
      Hydrogen bond information dumped for occupancies > 0.00

        DONOR ACCEPTORH ACCEPTOR
  atom# :res_at_atom atom# :res_at_atom atom# :res_at_atom %occupied distance angle
---------------- --------------------------------- ---------------------------- ---------

Can anyone help me with this. Any suggestions and comments will be highly
appreciated.

With best regards,
Anshul Awasthi

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