[gmx-users] Adding residue to .rtp file

Raji raji.phy at gmail.com
Wed Oct 31 15:56:18 CET 2018

Thank you for your valuable inputs. Yes i did checked ether
parameters, diethylether have O-C (alkyl) bonding parameter as CC32A
OC30A CC32A. but i dont find a parameter related to C(aromatic)-O
bonding. similar one is tyrosine CA-OH1, but it may need validation on
torsion terms?? can you please provide me information on how to do
validation calculation systematically for bonding parameter as well on

Thank you for your time.


>* Hi
*>>* 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.


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