Mr. Simmerling,
I totally overlooked this command and assumed that I would not be able to
tell which residue would have the free unit head or unit tail (and so would
not be able to specify exactly which atoms to connect using the bond
command). I did just look at the Amber 20 manual and I saw that the
sequence {A B C ...} connects the tail of A to the head of B, so on and so
forth. So I will know which one is which- thanks for your suggestion! I
will try to run this in tLEaP and let you know if any errors arise.
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 - 15:00:02 PST
