AMBER Archive (2009)

Subject: [AMBER] error in kclust of MMTB_tool set

From: kureeckal ramesh (kureeckalramesh_at_yahoo.co.in)
Date: Tue Nov 10 2009 - 06:41:31 CST

Hi AMBER users
I am performing cluster analysis for my protein [(total amino acids = 151) which has undegone MD simulations using AMBER],  using kclust of MMTSB tool

(i) I am getting an error while running kclust command of MMTSB_tool set.
(ii) The above analysis is done after stripping the water molecules from the protein using ptraj command of AMBER10

The output I got from kclust is as follows :
----------------------------------------------------------------------------------------------------------
../kclust -mode rmsd -centroid -cdist -heavy -lsqfit -radius 6 -maxerr 1 -iterate ../clustfils > ../Centroid_6

output
number of atoms do not match in file fix_numbering_pdb.csh (0, expected: 22422

--------------------------------------------------------------------------------------------------------------------
As I
am stuck at this step, I am not able to proceed further with cluster analysis. Desperately in need of help.

With regards
Ramesh K V

--- On Mon, 9/11/09, kureeckal ramesh <kureeckalramesh_at_yahoo.co.in> wrote:

From: kureeckal ramesh <kureeckalramesh_at_yahoo.co.in>
Subject: [AMBER] error in kclust of MMTB_tool set
To: amber_at_ambermd.org
Date: Monday, 9 November, 2009, 5:40 AM

Hi AMBER users
I am performing cluster analysis for my protein using kclust of MMTSB tool
(i) I am getting an error while running kclust command of MMTSB_tool set.
(ii) The above analysis 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

output
number of atoms do not match in file fix_numbering_pdb.csh (0, expected: 22422

--------------------------------------------------------------------------------------------------------------------
I am not able to proceed further with cluster analysis. I appreciate if the amber users could provide me the solution to overcome this problem

With regards
Ramesh K V

From: kureeckal ramesh <kureeckalramesh_at_yahoo.co.in>
Subject: [AMBER] error in kclust of MMTB_tool set
To: amber_at_ambermd.org
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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