Dr. Simmerling,
I would like to preface my update with an apology- another member of this
community has informed me that I have been referring to you by an
inappropriate title. While I should have been able to determine your title
from your signature line, I did not want to make any assumptions- I would
like to apologize for that and assure you that I meant no disrespect.
When running my script via tLEaP, the sequence {} command also gives the
same segmentation fault error as if I had run it via xLEaP instead. At this
point I am pretty stumped as to what might be causing this problem, or what
information might be helpful to solve this problem.
Any help is much appreciated,
-NDB
On Thu, Feb 24, 2022 at 4:07 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> there is a bond command in tleap that I use when adding bonds...
>
> On Thu, Feb 24, 2022 at 5:05 PM Nathan Black <nathanblack262.gmail.com>
> wrote:
>
> > Mr. Simmerling,
> >
> > As far as I am aware, I do need the graphical version. The reason for my
> > manual selection of C10/C11 atoms after the "> edit ULVm" command is so
> > that I can see the C10/C11 polymerization chain (C10/C11 are the unit's
> > tail and head, respectively) highlighted in purple after I use the
> sequence
> > {} command. That way, I can use "Edit > Show selection only" to eliminate
> > the other atoms from view. I want to do this so I can draw a bond between
> > the terminal ends of the polymerized chain (my end goal is to form a
> > polymerized "ring") without obfuscation by other atoms.
> >
> > My attempt did go far enough to generate a leap.log file, which was
> > attached to my original email along with my associated inputs. I do
> suppose
> > if there were a way to accomplish my goal using tLEaP over xLEaP, that
> > would be preferable- but I am not aware of any such workarounds.
> >
> > All the best,
> > NDB
> >
> > On Thu, Feb 24, 2022 at 3:49 PM Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > the lack of response might be due to the low number of people that use
> > > xleap. Do you need the graphical version, or would tleap do what you
> > need?
> > > with leap errors it can help to see if it got far enough to produce a
> > > leap.log file.
> > >
> > > On Thu, Feb 24, 2022 at 4:41 PM Nathan Black <nathanblack262.gmail.com
> >
> > > wrote:
> > >
> > > > Hello AMBER Users,
> > > >
> > > > I intend to use LEaP to polymerize a set of surfactants using the
> > > sequence
> > > > {} command. However, when I use this command, LEaP crashes and gives
> an
> > > > error message along the lines of:
> > > >
> > > > /usr/local/amber20/bin/xleap: line 12: 8121 Segmentation fault
> > > (core
> > > > dumped) $AMBERHOME/bin/xaLeap -I$AMBERHOME/dat/leap/prep
> > > > -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm
> > > > -I$AMBERHOME/dat/leap/cmd $*
> > > >
> > > > The number between "line 12:" and "Segmentation fault" differs
> between
> > > each
> > > > attempt. I have looked through other reports of this issue in the
> AMBER
> > > > Mailing List Archive, but it looks as though they have gone
> unresolved.
> > > >
> > > > I utilized an xLEaP script to form each surfactant and assign the
> > > head/tail
> > > > atoms for surfactant polymerization into micelles, but the actual
> > > > polymerization step is performed manually. The script runs without
> > issue,
> > > > it is only when I use the sequence {} command to polymerize the
> > > surfactants
> > > > that the segmentation fault is encountered. I have attached a clean
> > > > (single-attempt) leap.log file, the xLEaP script which was run, and
> any
> > > > files upon which it is dependent. Also below are the manual steps
> which
> > > are
> > > > performed after execution of the script.
> > > >
> > > > >edit ULVm
> > > >
> > > > Unit > Check unit > "Unit is OK."
> > > > Unit > Calculate net charge > "Total perturbed charge: -0.999997"
> > > > Display > Names
> > > > Select C10, C11 (manual click)
> > > > Unit > Close
> > > >
> > > > >ULVp = sequence {ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm ULVm
> > ULVm
> > > > ULVm ULVm ULVm ULVm ULVm ULVm ULVm}
> > > >
> > > > The above sequence {} command causes xLEaP to terminate and give the
> > > > segmentation fault error message. The machine this error occurred on
> > runs
> > > > CENTOS 7 and has Amber 20 installed, though I was able to recreate
> the
> > > > error on another machine running CENTOS 7 with Amber 18 installed.
> > > >
> > > > Any assistance is greatly appreciated!
> > > > -NDB
> > > > _______________________________________________
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Received on Thu Feb 24 2022 - 17:00:02 PST
