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.O :6.N out dist-init1
distance distance2 :3.O :7.N out dist-init2
distance distance3 :4.O :8.N out dist-init3
distance distance4 :5.O :9.N out dist-init4
distance distance5 :6.O :10.N out dist-init5
distance distance6 :7.O :11.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.atom atom# :res.atom atom# :res.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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Received on Fri Oct 15 2004 - 19:53:00 PDT
