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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> > >
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Received on Thu Feb 24 2022 - 14:30:02 PST
