Dear AMBER users
(1) I am working with the AMBER tutorials titled " Ligand Binding using MM and QMMM techniques." available at
http://www.rosswalker.co.uk/tutorials/psc_workshop/contents.htm.
(2) Though the tutorial recommends, AMBER 9 , I am working with AMBER 10. assuming that this exercise should also work for AMBER 10 as it is an updated version
(3) While I could complete few of the initial steps; i.e, using tleap for protein, I have got error when I executed similar type of command for ligand
(4) The error is pasted below:
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[root.server exe]# ./tleap -f taz_setup.leapcmd
+ /usr/local/amber10/bin/teLeap -I/usr/local/amber10/dat/leap/prep -I/usr/local/amber10/dat/leap/lib -I/usr/local/amber10/dat/leap/parm -I/usr/local/amber10/dat/leap/cmd -f taz_setup.leapcmd
-I: Adding /usr/local/amber10/dat/leap/prep to search path.
-I: Adding /usr/local/amber10/dat/leap/lib to search path.
-I: Adding /usr/local/amber10/dat/leap/parm to search path.
-I: Adding /usr/local/amber10/dat/leap/cmd to search path.
-f: Source taz_setup.leapcmd.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./taz_setup.leapcmd
----- Source: /usr/local/amber10/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber10/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
Loading parameters: ./TAZ.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading Mol2 file: ./TAZ.mol2
Reading MOLECULE named TAZ
../tleap: line 9: 8766 Segmentation fault /usr/local/amber10/bin/teLeap -I/usr/local/amber10/dat/leap/prep -I/usr/local/amber10/dat/leap/lib -I/usr/local/amber10/dat/leap/parm -I/usr/local/amber10/dat/leap/cmd $*
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(6) I tried with xleap also, but ended with the same type of error
(5) I request you to guide me in solving this error. Should I use only AMBER 9 for this type of exercise or can I use AMBER 10. Please suggest any other alternative
with regards
Ramesh K V
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Received on Mon Jul 06 2009 - 11:06:03 PDT
