I suspect that when you loadpdb, leap is assigning terminal residue
types by default since the bond isn't there already, due to 'residue
name mapping' (doesn't happen when you cyclize in xleap :-)
There was a recent post about how to turn off the residue mapping. An
easier way to override for a short sequence is to use 'loadpdbusingseq'
in leap. You may have to create the bond explicitly in leap after
loading pdb as well - not sure if the CONECT records are used (been out
of the office).
Bill
On 10/21/16 11:21 AM, David A Case wrote:
> 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 - 12:30:02 PDT
