Dear Matias,
Thank you so much! In fact, it was the issue with the empty spaces at
the end of some lines...
I would never figure that out myself. I was checking whether the format is
positional or not (as in PDB files for instance).
Best regards,
Dawid Grabarek
PS I still get the error regarding missing parameters but I will create a
separate thread on that. But I'll do it
tomorrow. It's almost midnight here in Poland :).
pon., 7 paź 2019 o 23:36 Matias Machado <mmachado.pasteur.edu.uy>
napisał(a):
> Dear Dawid,
>
> Did you edited the lib by hand to add SYN? Can you share the lib file you
> are using?
>
> I had a similar problem some time ago and it turned out to be a bad file
> format...
>
> In particular:
>
> + every line must end with NO extra space character or leap will stuck
> during the library loading
> + lines not starting with "!" must begin at the 2nd character or more
> (i.e. one or more space characters)
>
> Hope this helps...
>
> Best,
>
> Matias
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Dawid das" <addiw7.googlemail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Lunes, 7 de Octubre 2019 9:31:01
> Asunto: Re: [AMBER] tleap hangs when tries to read new residue
>
> Yes, the cpu is 100 % but there are no further results. I looked at
> leap.log but it does not report on any
> warnings/errors regarding the SYN residue.
>
> I have tried to load my protein with SYN removed from PDB and *.lib files
> and it works (in some sense,
> because I get a bunch of errors about missing parameters for virtually
> every protein atom except
> for peptide bond carbons). Anyway, let's just leave it for now, because the
> issue with SYN
> is related to the *.lib file.
>
> Best wishes,
> DG
>
> pon., 7 paź 2019 o 11:52 Bill Ross <ross.cgl.ucsf.edu> napisał(a):
>
> > If you see cpu at 100% while results remain 0%, I will make a convert of
> > you yet. I don't remember the debug stuff. Did you look at leap.log?
> > Debugging is about isolating, e.g. your res in it's own file. Or go to
> the
> > source, and say Darth sent you. :-)AI:
> > http://phobrain.com/pr/home/view.html
> > -------- Original message --------From: Dawid das <addiw7.googlemail.com
> >
> > Date: 10/7/19 2:40 AM (GMT-08:00) To: AMBER Mailing List <
> > amber.ambermd.org> Subject: Re: [AMBER] tleap hangs when tries to read
> > new residue Dear Bill,Thank you for your answer. I have checked my
> topology
> > and it looks fine.Is it possibly to make tleap produce more output data
> > (make it moreverbose/noisy)?Perhaps it would let me to find the source of
> > this issue.Best wishes,Dawid Grabarekniedz., 6 paź 2019 o 21:49 Bill
> Ross <
> > ross.cgl.ucsf.edu> napisał(a):> Better to put your own res in its own
> > file too.>> Bill>> On 10/6/19 12:48 PM, Bill Ross wrote:> >> > Sounds
> like
> > you may have a topological problem in your residue> > definition that
> > causes an infinite loop.> >> > Bill> >> > On 10/6/19 10:09 AM, Dawid das
> > wrote:> >> Dear Amber Users,> >>> >> I have a protein which contains a
> > modified amino acid (SYN) that is> >> covalently bonded to both
> proceeding
> > and following natural amino acids.> >>> >> Now, I have the parameters
> ready
> > for SYN so I put them into> >> the parm99.dat file. Also, I have defined
> > the SYN in my library> >> file (all_amino94ildn.lib) together with all
> the
> > other amino acids.> >>> >> When I run> >> tleap -f tleap.in > tleap.out>
> > >>> >> it hangs while loading the amino acids library:> >> Loading
> > library:> >>
> > /home/dawid/Programy/AmberTools/amber18/dat/leap/lib/all_amino94ildn.lib>
> > >> Loading: ALA> >> Loading: ARG> >> Loading: ASH> >> Loading: ASN> >>
> > Loading: ASP> >> Loading: CYM> >> Loading: CYS> >> Loading: CYX> >>
> > Loading: GLH> >> Loading: GLN> >> Loading: GLU> >> Loading: GLY> >>
> > Loading: HID> >> Loading: HIE> >> Loading: HIP> >> Loading: ILE> >>
> > Loading: LEU> >> Loading: LYN> >> Loading: LYS> >> Loading: MET> >>
> > Loading: PHE> >> Loading: PRO> >> Loading: SER> >> Loading: SYN> >>> >>
> It
> > always happens at this stage. I have tried to create a separate> >>
> library
> > for SYN residue and use loadOff but then I get an error message> >>
> saying
> > that atom types for SYN are unknown even though I have defined> them.>
> >>>
> > >> What could be the source of this issue?> >> I attach my tleap.in
> > file.> >>> >> Best wishes,> >> Dawid Grabarek> >>> >>
> > _______________________________________________> >> AMBER mailing list>
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Received on Mon Oct 07 2019 - 15:00:02 PDT
