Dr. Simmerling and other AMBER Users,
Attached to this email is my tLEaP script, as well as all necessary
dependencies. I will provide some context to my larger project and then for
each file, in case that helps anyone to understand my files while trying to
reproduce the issue.
My larger project involves the modeling of polymerized micelles composed of
surfactants with amino acid headgroups. Their tails are based upon
undecylenic acid (general organic domain), while their heads are standard
amino acid residues. Thus, I have elected to describe the surfactant tail
with the GAFF2 force field, and the surfactant head with the FF14SB force
field.
Context for each attached file:
*dipeptide_run_step4_amber20* is the actual script which, when called, runs
tLEaP and inputs the commands found in
dipeptide_step4_leap_generate_monomer_units_amber20.in.
*dipeptide_step4_leap_generate_monomer_units_amber20.in
<
http://dipeptide_step4_leap_generate_monomer_units_amber20.in> *contains
the tLEaP commands which are input by dipeptide_run_step4_amber20. I have
debugged far enough to find that the final sequence {} command near the end
is what is causing the segmentation fault error. All subsequent lines have
been commented out.
*dipeptide_UNA.prepin* is the AMBER prep file corresponding to the
surfactant tail. It is loaded so that it can be combined with amino acid
residues,
*dipeptide_UNA.frcmod* contains any missing parameters for the surfactant
tail as needed before combining it with amino acid residues to form the
full surfactants. The tail itself is described completely by GAFF2,
however, so this file should be empty.
*dipeptide_surfactant_tail_head_boundary.frcmod* contains the
manually-input parameters meant to satisfy the surfactant head-tail
boundary (where the regions described by GAFF2 and FF14SB meet).
If other information is needed to assist anyone in recreating the error, I
am more than happy to provide that.
Much appreciated,
-NDB
On Fri, Feb 25, 2022 at 10:03 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it doesn't look like any of the files that you shared have a sequence
> command. if you can share just the files needed to run tleap and get the
> error it may be helpful to people trying to reproduce the problem.
> it looks, though, that what you're doing is a pretty advanced project
> that's difficult for others to follow in detail, and it's likely that
> you'll need to do debugging work yourself to reproduce the error with a
> simpler setup before anyone can help.
>
> On Thu, Feb 24, 2022 at 7:33 PM Nathan Black <nathanblack262.gmail.com>
> wrote:
>
> > Dr. Simmerling,
> >
> > I would like to preface my update with an apology- another member of this
> > community has informed me that I have been referring to you by an
> > inappropriate title. While I should have been able to determine your
> title
> > from your signature line, I did not want to make any assumptions- I would
> > like to apologize for that and assure you that I meant no disrespect.
> >
> > When running my script via tLEaP, the sequence {} command also gives the
> > same segmentation fault error as if I had run it via xLEaP instead. At
> this
> > point I am pretty stumped as to what might be causing this problem, or
> what
> > information might be helpful to solve this problem.
> >
> > Any help is 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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> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
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Received on Fri Feb 25 2022 - 09:30:02 PST
