Dear Chris,
Did you look at the q4md-fft tutorials?
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
&
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
& even
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
(we recently made this procedure even more simple thanks to the help
of the R.E.D. Server users...)
Now, if you have a big molecule with a peptide bond, and you want to
split this molecule into two elementary building blocks by adding the
ACE & NME caps, below is the principle; check that peptide bonds are
all trans (except if you choose it)
O O 2 INTRA-MCC O
...C-N... --> ...C-NME ACE-N... --> ...C N...
H H H
2 building blocks 2 fragments to be connected
in LEaP
if something is not clear, do not hesitate to ask more questions...
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#Fig1
to create prmtop/prmcrd files using Ante_R.E.D./R.E.D./R.E.D. Server
regards, Francois
> I am trying to use R.E.D.S to build force field libraries for a non
> standard serine residue, which is covalently bonded to a drug. However, I
> am having trouble placing the ACE and NME capping groups. I have read
> through the this
> <http://ambermd.org/tutorials/basic/tutorial1/section2.htm>tutorial on
> Amber but my problem is 1) I cannot create .prmtop and .inpcrd
> files from a non standard residue, and 2) the computing cluster I am on
> does not support graphical interfacing so I am stuck using only tleap,
> which this tutorial does not discuss. Could anyone provide me methods
> which they have used to cap residues with ACE and NME that don't involve
> the use of xleap or the need to build prmtop and inpcrd files?
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Received on Fri Jan 13 2012 - 23:30:03 PST
