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> >>> >>
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Received on Mon Oct 07 2019 - 15:00:02 PDT
