Hello AMBER Users,
It turns out that removing the saving library files process from the
amber20.in file led to a resolution to the segmentation fault error, not
the head/tail flip as I initially thought. Perhaps the file was too big and
accessing too much memory at once with all the open files and residues?
Much appreciated,
NDB
On Mon, Feb 28, 2022 at 10:02 AM Nathan Black <nathanblack262.gmail.com>
wrote:
> Dr. Horn, Dr. Simmerling, and other AMBER Users,
>
> I believe I have solved the issue through debugging. The issue was
> resolved when I redefined (and flipped) the designated "head" and "tail" of
> my surfactant units. I think that I was attempting to polymerize them in a
> way that violated a carbon atom's valence.
>
> Initially, the combine {} command (as implemented in the copy/combine/bond
> approach suggested by Dr. Horn) was also giving me a segmentation fault
> error, but this head/tail switch fixed that error as well.
>
> Thank all of you for your assistance. It is much appreciated,
> NDB
>
> On Sun, Feb 27, 2022 at 2:53 PM Dr. Anselm Horn <anselm.horn.fau.de>
> wrote:
>
>> Nathan,
>>
>> although you still might simplify your leap input further accroding to
>> Carlos' suggestion to localize the problematic point in your input more
>> clearly,
>> I had a quick look at your debug6 file that caused the segmentation fault.
>>
>> If I understood correctly, you first build your surfactant molecule ULVm
>> as a sequence of three residues, two of which are terminal ones, your
>> own UNA and CVAL. After saving this new entity, you seem to modify it
>> afterwards (designating new head and tail atoms).
>> And then you try to build a new molecules via the sequence command,
>> where you use the three-residue-molecule created in the first step and
>> modified afterwards as a recurring building block.
>>
>> Still, I do not know what your polymeric structure looks like (sorry for
>> that), so it's not clear to me, which units you intend to create and
>> polymerize.
>> Since you used the terminal residue CVAL in your first building block,
>> it seems to me, however, that there this might me one problem: the
>> seuqence command tries to form covalent bonds between the residues, and
>> clearly terminal residues are not well suited for that. So there will be
>> a problem from CVAL of one ULVm to the next.
>>
>> I can only speculate: If your idea is to setup a large macromolecule
>> that consists of many covalently joined linear building blocks your
>> ansatz is correct, generally. But, as Carlos pointed out, that's a
>> complicated system with many sources of errors.
>> - The building blocks must not contain terminal residues (in-script
>> modifications do not account for different parameters or number of atoms)
>> - I never used the sequence command on a derived and modified unit, does
>> this work?
>> - Is the building block in the sequence command actually always a *new*
>> unit (like a new instance of a variable) or just the identical unit
>> written in a sequence command (which would explain the error)? Maybe the
>> commands copy, bond and combine could be of use there: You have to try
>> out, but use mini-steps.
>> - Of course, you'd need terminal residues for your sequence.
>>
>> If your idea is to setup a large system of three-residue molecules, then
>> the sequence command is the wrong path IMHO.
>>
>> Again, as Carlos pointed out, you system is very complex. Try to
>> simplify the single steps further to locate the very position of the
>> problem, but also check whether the output you obtain is what you
>> intended.
>>
>> Maybe that helps.
>>
>> Best,
>>
>> Anselm
>>
>> Bioinformatik | NHR.FAU
>> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
>> Germany
>>
>>
>>
>>
>> On 02/25/2022 09:50 PM, Nathan Black wrote:
>> > Dr. Simmerling and other AMBER Users,
>> >
>> > I implemented the changes you suggested and created cleaner debug files.
>> >
>> > I then tested the process of saving parameter topology and coordinate
>> files
>> > of three different surfactants (no polymerization): ULV (tail + leucine
>> +
>> > c-terminal valine), UGA (tail + glycine + c-terminal alanine), and UAA
>> > (tail + alanine + c-terminal alanine) to see if the error was
>> > residue-dependent. Each surfactant's files were saved without issue. I
>> have
>> > not yet tested the effects of running MD simulation(s) with these files.
>> >
>> > Afterwards, I tested the sequence {} command on polymerizing ULV
>> > surfactants. I found that if the sequence was longer than two ULV
>> > surfactants (i.e., the sequence {} command) contained three or more
>> > surfactants, the sequence {} command would cause a segmentation fault
>> > error.
>> >
>> > Attached are three tLEaP scripts, along with the same dependencies as
>> sent
>> > before. Each of the tLEaP scripts is dependent on the same files:
>> >
>> > The script with the tag "debug1" deals with saving files for the ULV
>> > surfactant on its lonesome. It ran without issues on my machine.
>> >
>> > The script with the tag "debug4" deals with saving files for a 2-mer ULV
>> > surfactant polymer. This also ran without issues on my machine.
>> >
>> > The script with the tag "debug6" deals with saving files for a 3-mer ULV
>> > surfactant polymer. The sequence {} command caused a segmentation fault
>> > error on my machine (CENTOS 7, Amber 20).
>> >
>> > Hopefully, this is helpful to anyone trying to recreate this error.
>> >
>> > All the best,
>> > NDB
>> >
>> >
>> >
>> >
>> >
>> > On Fri, Feb 25, 2022 at 11:21 AM Carlos Simmerling <
>> > carlos.simmerling.gmail.com> wrote:
>> >
>> >> 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 Mon Feb 28 2022 - 09:00:02 PST
