Hi,
You could use R.E.D. Server .
http://q4md-forcefieldtools.org/REDS/ to
(i) build the dipeptide (for your modified amino-acid) (ii) derive
charges & build force field libraries for the different molecular
fragments required.
See
http://q4md-forcefieldtools.org/REDS/faq.php
- In particular:
http://q4md-forcefieldtools.org/REDS/faq.php#20
http://q4md-forcefieldtools.org/REDS/Demo-jmol/Applet2.html
to build the initial dipeptide
- and
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25 (all automatic)
versus
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
to derive charges & build force field libraries for the different
molecular fragments required.
regards, Francois
Quoting "George A. Khoury" <gkhoury.princeton.edu>:
> Hello:
>
> I have made a mutation in position 1 of a peptide chain (by stripping out
> the side chain and adding my new amino acid which I have parameters for) to
> an unnatural amino acid.
> The unnatural amino acid was built using residuegen and I am building
> everything using xleap.
> Upon looking at the structure, I noticed that my N-terminus has only 1
> hydrogen instead of the usual 3. It is my understanding that in the natural
> amino acids a residue at the N-terminus (i.e. Ala) will be replaced by a
> NAla, which will have the proper valence for the N-terminus.
>
> I have tried several different things including changing my prep file from
> OMIT to NOMIT so that the beginning dummy atoms are not omitted, but that
> did not seem to work.
>
> Is it possible to do something similar for my unnatural amino acid to what
> is done for the natural amino acids in AMBER? If so, could someone tell me
> what I could do to proceed? Thanks in advance for your help and have a good
> day.
> Best,
> George
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Received on Tue Sep 06 2011 - 08:30:02 PDT
