On Fri, Oct 21, 2016, Thakur, Abhishek wrote:
>
> But as soon as I am solvating it and making prmtop, inpcrd and pdb it
> seems that N terminal is breaking bond and making it -NH3
Bonds never break in molecular mechanics calculations. Are you sure that you
have the correct bond there in the starting structure?
Where are the hydrogens coming from to "make it NH3"???? You can't be
breaking bonds are making new ones if you are doing ordinary simulations.
I have a feeling that this email exchange is not helping you very much. Your
very short verbal descriptions of what you have done are hard for others to
understand. For example, I don't know what you mean when you say "making bond
in gaussian".
I'd suggest this: take an X-ray structure of a cyclic peptide (it
won't be "your" sequence, but this is a learning procedure). Build it in leap
(using the steps outlined earlier--you now have a good starting structure).
Run simulations enough so that you are comfortable with the procedure and the
results. You will then have a reference calculation that works, and you will
be able to use it to help debug problems you may have in the sequence of
interest.
...good luck....dac
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Received on Fri Oct 21 2016 - 11:30:03 PDT
