[gmx-users] Adding residue to .rtp file

[Justin Lemkul]

On 10/30/18 12:12 PM, Raji wrote:
> 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.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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