Hi Amber,
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?
Thanks in advance,
Chris Bryant
--
Chris Bryant
Biochemistry B.S.
Philosophy B.A.
Vice President, Alpha Chi Sigma
Case Western Reserve University 2013
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Received on Fri Jan 13 2012 - 12:00:02 PST
