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 Sun Oct 06 2019 - 13:00:02 PDT
