Dear Amber community members,
I, Vaibhav A. Dixit a Ph.D. scholar at NIPER, SAS Nagar, INDIA, am beginner
with AMBER10 package. I'm trying the AMBER tutorials for free energy
perturbation calculations.
In this regard I'm facing problems with the antechamber (sustiva)
tutorialnecessary to generate parameters for organic small molecules
http://ambermd.org/tutorials/basic/tutorial4b/
While loading the mol2 file using loadmol2 command in tleap I'm
getting segmentation
fault. I tried to recompile tleap, but that also did not work and gave the
same error.
Could anyone suggest on what is going wrong and how to fix that and is
recompiling tleap or leap is necessary in this case? Waiting for some
insightful comments and suggestion... thank you all
Following is the segmentation fault details (at the end) and initial part is
how I got there.
----------------------------
[vaibhav.localhost antechamber]$ tleap -f leaprc.ff99SB
-I: Adding /home/vaibhav/software/amber10/dat/leap/prep to search path.
-I: Adding /home/vaibhav/software/amber10/dat/leap/lib to search path.
-I: Adding /home/vaibhav/software/amber10/dat/leap/parm to search path.
-I: Adding /home/vaibhav/software/amber10/dat/leap/cmd to search path.
-f: Source leaprc.ff99SB.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: /home/vaibhav/software/amber10/dat/leap/cmd/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /home/vaibhav/software/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters:
/home/vaibhav/software/amber10/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library:
/home/vaibhav/software/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /home/vaibhav/software/amber10/dat/leap/lib/all_amino94.lib
Loading library:
/home/vaibhav/software/amber10/dat/leap/lib/all_aminoct94.lib
Loading library:
/home/vaibhav/software/amber10/dat/leap/lib/all_aminont94.lib
Loading library: /home/vaibhav/software/amber10/dat/leap/lib/ions94.lib
Loading library: /home/vaibhav/software/amber10/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /home/vaibhav/software/amber10/dat/leap/cmd/leaprc.gaff
----- Source of /home/vaibhav/software/amber10/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/vaibhav/software/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June,
2003)
> SUS = loadmol2 sustiva.mol2
Loading Mol2 file: ./sustiva.mol2
Reading MOLECULE named SUS
/home/vaibhav/software/amber10/exe/tleap: line 8: 4080 Segmentation
fault /home/vaibhav/software/amber10/bin/teLeap
-I/home/vaibhav/software/amber10/dat/leap/prep
-I/home/vaibhav/software/amber10/dat/leap/lib
-I/home/vaibhav/software/amber10/dat/leap/parm
-I/home/vaibhav/software/amber10/dat/leap/cmd $*
[vaibhav.localhost antechamber]$
----------------------------------------------------------------------
---------
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Thu May 13 2010 - 03:30:05 PDT
