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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Feb 24 2022 - 14:30:02 PST
