[gmx-users] Adding residue to .rtp file

[Raji]

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?

2. Charge of Hydrogen atoms (removed) are balanced over the oxygen and
alkyl carbon is that the right approach?

        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?


Thanks

Raji


> Date: Mon, 29 Oct 2018 21:13:34 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Adding residue to .rtp file
> Message-ID: <db1dd72e-3c7d-2eba-7529-dd33e29f26bb at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 10/24/18 2:46 PM, Raji wrote:
> > Thank you for your reply. I have few more questions
> > 1. Yes, command pdb2gmx continued and generated the topology. The warning
> > is about 74 atoms which are from the new added rtp entry. I just want to
> > understand more about the warning. I dont find any related information?
>
> Low or zero experimental occupancies indicate potentially problematic
> coordinates. If you're simply modeling in coordinates, the warning is
> irrelevant.
>
> > 2. What is the significance of the atom types in the rtp file?
> > for example
> > CTL3 - carbon of methyl group
>
> This is from the lipid force field.
>
> > CG331 - Aliphatic C for methyl group
>
> This is a CGenFF type (any type with "G" as the second character is from
> CGenFF.
>
> > What is the difference between them and How to choose the right one for
> > carbon in alkyl chain?
>
> An alkyl chain on an amino acid should use CT1, CT2, CT3 (see existing
> amino acids).
>
> -Justin
>
>
>