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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>
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Received on Thu Feb 24 2022 - 14:00:04 PST
