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 - 14:00:03 PST
