AMBER Archive (2009)

Subject: [AMBER] ptraj script for H bond for protein (explicit )

From: kureeckal ramesh (
Date: Sat Nov 07 2009 - 01:38:29 CST

Hi AMBER users
 We have performed MD simulations for a protein under explicit conditions. Though we are able to get the output for H bond analyis for the protein (after stripping the water molecules), the report is huge. As I understand from the report., it is displaying the information of H bond formed between the oxygen atom of solvent and different atoms of the amino acid residues.

I would be interested in having H bond analysis done between various atoms of the residues (for eg: as it is done for TRPcage protein of the AMBER tutorial). I feel the ptrag script (analyse_hbond.ptraj)should be modified. But I do not know how to do it. I would appreciate if you can give me a clue for doing the above analysis .

Thanking you in advance
Ramesh K V

--- On Fri, 6/11/09, kureeckal ramesh <> wrote:

From: kureeckal ramesh <>
Subject: [AMBER] error in kclust of MMTB_tool set
Date: Friday, 6 November, 2009, 1:03 PM

Hi AMBER users

(i) I am getting an error while running kclust command of MMTB_tool set.
(ii) The above anlysis is done after stripping the water molecules from the protein using ptraj command

The output I got from kclust is as follows :
../kclust -mode rmsd -centroid -cdist -heavy -lsqfit -radius 6 -maxerr 1 -iterate ../clustfils > ../Centroid_6
number of atoms do not match in file fix_numbering_pdb.csh (0, expected: 22422


Kindly suggest me the solution for overcoming this error

Thanking in advance
Ramesh K V

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