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 more
verbose/noisy)?
Perhaps it would let me to find the source of this issue.
Best wishes,
Dawid Grabarek
niedz., 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 - 03:00:02 PDT
