Dear Dr Case,
> My take (others, especially FyD may wish to elaborate):
>
> It *is* possible to use antechamber for non-standard amino acids (see option
> 2 here: http://ambermd.org/antechamber/example.html), but it is way too
> complex (this example has seven steps). RED also has a learning curve, but
> has lots of examples and authors who are willing to provide help and advice.
In R.E.D. Server, one can by now build the 2 terminal & the central
fragments for a modified amino-acid or a modified nucleotide directly
from a _single_ dipeptide or nucleoside molecule (a single P2N file),
respectively. No need anymore to add the methylammonium, acetate
and/or dimethylphosphate molecules (internally stored) and no need to
define the constraints during the charge fitting step to design the
fragments (automatically added); all is handled by the server...
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
&
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#27
We will continue to develop such 'simplified' protocols for users...
regards, Francois
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Received on Sat Nov 05 2011 - 00:30:03 PDT
