On Mon, Feb 22, 2016, Jesmita Dhar wrote:
> I want to simulate a complexed protein docked
> with a peptide that contain an isoaspartic acid. I have used
> antechember. But the parameter file I got, can not be used to generate
> topology file for the complexed protein using leap.
This is going to be really hard to debug via email. Generally:
1. If you are going to link the ISA residue with other standard peptide units,
you should use antechamber with Amber atom types, not gaff types.
2. Try to use LEaP on just the peptide first, not the whole complex.
3. Setting up modified amino acids (for inclusion in a peptide) is rather
different than for a standard ligand. See tutorial B5 for an example.
These should get you started in the correct direction. But this is a fairly
hard problem, so expect to do a lot of trial and error to get things right.
...dac
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Received on Mon Feb 22 2016 - 05:00:06 PST
