I took a look at this, but like I mentioned before this is quite complex
and there is a lot going on. It seems like you should be able to simplify
this a lot - reduce the number of different monomers that you're creating,
and so on. If you can reproduce the problem in a small test case then it
would be far easier to consider working through it. Right now this looks
like a very complex project, and you can probably do a lot of the
debugging on your own. One step could be to make sure that you can build
and simulate these as monomers, and then try to build a 2-unit polymer and
see what happens. I also suggest removing anything that isn't actually
needed (it looks like the sequence command doesn't use a lot of the
monomers that you're building). It also might help to move the building of
monomer libraries to a different script.
On Fri, Feb 25, 2022 at 12:05 PM Nathan Black <nathanblack262.gmail.com>
wrote:
> 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
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Feb 25 2022 - 09:30:03 PST
