Dear Jason and Bill
Thank you for your help
On Sun, Apr 26, 2015 at 2:06 AM, Jason Swails <jason.swails.gmail.com>
wrote:
A developer would need to be able to reproduce this behavior in order to
help. Can you post your leap script and PDB file to an email so we can
take a look?
I at
ta
ch pdb file and other necessary file for
checking
this.
For your information
.
I recently install this AmberTool 14.25 in my system
that have no Amber 14. Earlier I am using the Amber 12 and AmberTool 13,
that is working very fine with the same process.
I also check the older pdb file with that I completed my simulation giving
the same error.
I am attaching the file through google drive, link is given
below(cho_Lac80wt).
cho_lac80wt
<
https://docs.google.com/folderview?id=0B27HoitrBN6aVXZmT1hGdnV0elk&usp=drive_web>
As always, it's a good idea to check your PDB file first (for instance, run
it through pdb4amber first, and try to visualize it with a program like VMD
or PyMol).
I check my pdb file in VMD that is looking good.
Loading parameters:
/home/rahman/sware/ambertool14/amber14/dat/leap/parm/frcmod.spce
Reading force field modification type file (frcmod)
One thing you could do is look at that file and make sure it isn't
corrupted.
I check this file by cat command and it is giving the following out put.
[rahman.localhost ~]$ cat
/home/rahman/sware/ambertool14/amber14/dat/leap/parm/frcmod.spce
This is the additional/replacement parameter set for SPC/E water
MASS
OW 16.0
BOND
OW-HW 553.0 1.0000 SPC/E water
HW-HW 553.0 1.6330 SPC/E water
ANGLE
DIHE
NONBON
OW 1.7767 0.1553
Thanks
Rahman
On Sat, Apr 25, 2015 at 10:56 AM, MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
wrote:
> Dear Amber Users
>
> I am trying to run the tleap in AmberTool 14.25, but I am getting
> segmentation fault error. After that I updated my amber14 and I got no new
> update is available for amber 14. given below
>
> [rahman.localhost amber14]$ ./update_amber --update
> Preparing to apply updates... please wait.
> Proxy Password:
> No new updates available for AmberTools 14
>
> The segmented error given below, the value of segmentation error are
> changing every time when I am running the command.
> [rahman.localhost leap]$ tleap -s -f leap.in
> -I: Adding /home/rahman/sware/ambertool14/amber14/dat/leap/prep to search
> path.
> -I: Adding /home/rahman/sware/ambertool14/amber14/dat/leap/lib to search
> path.
> -I: Adding /home/rahman/sware/ambertool14/amber14/dat/leap/parm to search
> path.
> -I: Adding /home/rahman/sware/ambertool14/amber14/dat/leap/cmd to search
> path.
> -s: Ignoring startup file: leaprc
> -f: Source leap.in.
>
> Welcome to LEaP!
> Sourcing: ./leap.in
> Loading parameters:
> /home/rahman/sware/ambertool14/amber14/dat/leap/parm/frcmod.spce
> Reading force field modification type file (frcmod)
> Reading title:
> This is the additional/replacement parameter set for SPC/E water
> */home/rahman/sware/ambertool14/amber14/bin/tleap: line 17: 7255
> Segmentation fault * (core dumped) $AMBERHOME/bin/teLeap
> -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib
> -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
> [rahman.localhost leap]$
>
> Thanks in advanced for your help.
> Regards
> Rahman
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Apr 26 2015 - 23:30:02 PDT
