[gmx-users] Adding residue to .rtp file
jalemkul at vt.edu
Wed Oct 31 13:54:28 CET 2018
On 10/30/18 12:12 PM, Raji wrote:
> Thank you for your input.
> 1. when attaching the alkyl chain with OH group in the aminoacid, to
> represent the bonded term C(aromatic)-O-C (alkyl). i took O as OC301 and
> C(alkyl) as CT2. But there is no bonded term for CA-OC301. How to import
> this by analogy?
Look into the ether parameters.
> 2. Charge of Hydrogen atoms (removed) are balanced over the oxygen and
> alkyl carbon is that the right approach?
As a first guess, I would just combine the H charge with the parent C.
But you'll need to do some basic validation of anything you do here.
> CZ CA 0.11 18
> OB OC301 -0.28 19 ;(in amino acid OH -0.54 HH 0.43)
> CH CT2 -0.01 20
> HH1 HA 0.09 21
> HH2 HA 0.09 22
> CI CT2 -0.18 23
> HI1 HA 0.09 24
> HI2 HA 0.09 25
> 3. Also i want to add n-terminal capping with carboxybenzyl for the
> peptide. If i use CGenFF parameters for the capping alone, how much it will
> affect the accuracy?
Again, if you've got something covalently bonded to the protein, you
should parametrize it thoroughly using core atom types in the force
field, not mixing CGenFF types into protein residues.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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