On Thu, Oct 20, 2016, Thakur, Abhishek wrote:
>
> I have tried to edit leaprc.ff14SB as per your suggestion
>
> 1. modify (a local copy of) the leaprc.protein.ff14SB file, removing the
> addPdbResMap block. This will tell leap that the beginning and ending
> residues are to be "non-terminal" residues (since that is what they will be
> after the cyclization).
>
> But stil it is not giving me cyclic structure.
Of course! Please see step 3 from my earlier email:
> 3. generate a reasonable starting structure for the cyclized peptide.
Amber is not a very good tool (generally speaking) for carrying out step 3.
If you Google on something like "generate cyclic peptide structure
coordinates", you will get some interesting leads.
....dac
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Received on Fri Oct 21 2016 - 05:30:04 PDT
