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
> >>>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> AMBER mailing list
> >>>>>>>> AMBER.ambermd.org
> >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> AMBER mailing list
> >>>>>>> AMBER.ambermd.org
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 28 2022 - 08:30:03 PST
