Re: [AMBER] phosphorylated peptide with implicit solvent

From: David A Case <>
Date: Fri, 9 Nov 2018 08:17:44 -0500

On Fri, Nov 09, 2018, 1342435023 wrote:
>I want to run a MD simulation for a phosphorylated peptide using
>implicit solvent, but I don't know where can I get proper force field
>parameters. Previously I was using the amber99sb-ildn force field for
>that peptide without phosphorylation.

You should source leaprc.phosaa10 in your tleap input file. See the comments
at the top of that file for instructions. Note that standard PDB residue
names are used for the 2- charge state, but we had to make up some new names
for the 1- state.

Two things to check: first, does amber99sb-ildn define new atom types? If
so, you may need to do some work to make things compatible with ff99sb-ildn.
(Sorry: I've never used ff99sb-ildn, so don't know in detail how it differs
from ff99sb itself.)

Second, I'm unsure how much to trust these parameters with implicit solvent.
Maybe people on the list will be able report on experiences they have had.

....good luck...dac

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Received on Fri Nov 09 2018 - 05:30:02 PST
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