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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- application/octet-stream attachment: tleap.in
Received on Sun Oct 06 2019 - 10:30:02 PDT
