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 Sun Oct 06 2019 - 13:00:03 PDT
