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.yahoo.co.in> wrote:
From: kureeckal ramesh <kureeckalramesh.yahoo.co.in>
Subject: [AMBER] error in kclust of MMTB_tool set
To: amber.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.yahoo.co.in>
Subject: [AMBER] error in kclust of MMTB_tool set
To: amber.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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Received on Tue Nov 10 2009 - 05:00:03 PST
