Thanks David.
I succesfully created the parameter file for isoaspartic acid
following the tutorial B5.
On Mon, Feb 22, 2016 at 6:27 PM, David A Case <david.case.rutgers.edu> wrote:
> 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 Tue Feb 23 2016 - 04:00:06 PST
