[gmx-users] termini modification

[lina]

pdb2gmx -ter

On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj <vijayaraj81 at gmail.com> wrote:
> Hello,
>
> I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the
> terminal residues from NALA and CALA to normal ALA (just as middle
> residues). As the terminal selection option is not enabled with the amber
> ff, I am using the termini modification parameters with aminoacids.c.tdb.
> here is my code for the aminoacids.c.tdb
>
> [ COO- ]
>
> [ replace ]
> H    H    1.00800        0.27190
> N    N    14.01000    -0.41570
> CA    CT    12.01000    0.03370
> HA    H1    1.00800        0.08230
> C    C    12.01000    0.59730
> CB    CT    12.01        -0.1825
> HB1    HC    1.008        0.0603
> HB2    HC    1.008        0.0603
> HB3    HC    1.008        0.0603
>
> [ add ]
> 1    1    O    C    CA    N
>         O    16.00000    -0.56790
>
> [ bonds ]
> C    O     1    0.12290        476976.0
>
> [ delete ]
> OC1
> OC2
>
>
> when I run pdb2gmx using this termini modification, everything works fine
> except the deletion of OC1 and OC2 atoms, the error which I get for this run
> as follows,
>
> Fatal error:
> Atom OC2 not found in residue seq.nr. 8 while adding atom
>
>
> any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [
> delete ] option with the aminoacids.c.tdb file, it works fine by adding the
> O atom to the terminal residue including the presence of OC1 and OC2 atoms.
> first I am trying to modify the c terminal residue.
>
> Regards,
> vijay.
>
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-- 
Best Regards,

lina