On Sat, Aug 17, 2013, onetwo wrote:
>
> I am using Amber to do the MD simulation of a peptide bound to a protein.
>
> I have docked this peptide to the protein, therefore its residue
> name has changed to UNK, and all the amino acids have became as one
> molecule. So, I have to first run antechamber before going to xleap.
Far easier is to just manually change the residue names back to their proper
values. (Aside: is it the docking program that did this? Which one?)
I suspect your antechamber problems came from giving it too large a molecule:
how big is the peptide?
But you will get a better force field if you use the Amber force field for
peptides (be sure to use ff12SB) than is you try to make antechamber provide
the parameters.
...dac
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Received on Mon Aug 19 2013 - 06:30:03 PDT
