[gmx-users] aminoacids.n.tdb

[Mark Abraham]

On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote:
>
> Hi Gromacs users,
>
> I want to covalently link the lauroic acid to the Valine residue (it 
> is a peptide (amide) bond), I know that I should update the 
> specbond.dat.But before updating this file, I need the NH as an N 
> terminal of the first residue (Valine).When I used pdb2gmx with the 
> –ter flag, I got either NH3, NH2 or None instead of NH.So, I add the 
> [NH] directive in the aminoacids.n.rtp file, as follows;
>
>
> [ NH ]
>
> [ replace ]
>
> ; old-namenew-typenew-massnew-charge
>
> NLN14.0067-0.31
>
> CACH113.0190.127
>
> [ add ]
>
> 12HNCAC
>
> ;atom_typemasscharge
>
> H1.0080.31
>
> [ delete ]
>
> H
>
> [ bonds ]
>
> NHgb_2
>
> [ angles ]
>
> CANHga_11
>
> [ dihedrals ]
>
> HNCACgd_29
>
>
> (ps. I wrote the charges of N, CA and H according to values defined in 
> topol.top and also I used the Gromos96 53a6 force field)
>
>
> Then, I used the pdb2gmx with –ter, I could see:
>
> Select start terminus type for VAL
>
> 0: NH
>
> 1: NH3+
>
> 2: NH2
>
> 3: None
>
>
> Finally, I got thetopol.top, posre itp and conf.gro files. But when I 
> looked into conf.gro, I see that I am getting “None”. How can I get 
> the NH ?
>

Coordinating multiple "moving parts" like the specbond and 
terminus-fixing is probably a recipe for trouble.

Since you have to make an .rtp entry for lauroic acid anyway, you can 
make one that uses backbone-style linking. Most of the forcefields will 
have examples of non-amino-acid terminating residues - these make a 
single peptide bond just like yours does. Now you can ignore the 
specbond and terminus-fixing mechanisms entirely.

Mark