On Thu, Oct 20, 2016, Thakur, Abhishek wrote:
>
> Thank you for your suggestion, I think I have a cyclic peptide of around
> 75 atoms, so I think that is why antechamber is not working.
To make a cyclic peptide, you have to three things (generally):
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).
2. add the "bond" command to the tleap input to create a bond between the C of
the last residue and the N of the first residue.
3. generate a reasonable starting structure for the cyclized peptide.
Step 3 has been discussed earlier. I think you missing Step 1, and hence
trying to make a bond between atom types C and N3, rather than C and N.
...hope this helps...dac
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Received on Thu Oct 20 2016 - 10:00:04 PDT
