Dear Case,
Thanks a lot for the reply.
I used Glide for docking, it converted whole peptide to one molecule. Otherwise peptide is of 5 amino acid in length only
I will try to manually change it to peptide again, and also will use the force field you specified.
Thanks again for the suggestion.
Regards
On Mon, 19 Aug 2013 18:44:10 +0530 wrote
>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 - 21:30:02 PDT
