[gmx-users] Special bond between metallic layers & protein

[Mark Abraham]

On Wed, Apr 23, 2014 at 3:18 PM, fantaman <nicola.staffolani at gmail.com>wrote:

> Hi everybody,
>
> for special reasons I am trying to simulate the interactions between a
> protein and 3 layers of platinum (PT) - actually I would like to fix the
> protein to the surface (= external layer) of the metal, but I am facing
> problems already in the pdb phase.
>
> In order to input the PT I have created a Protein residue called PT in
> residuetypes.dat and defined it as
>
> [ PT ]
>   [ atoms ]
>   PT    PT     0.00000     0
>
> in top/gromos43a1.ff/aminoacids.rtp (of course gromos43a1.ff is the force
> field I am using) with only one atom and then I enter in the pdb file all
> the PT atoms as different residues (→ 1 atom, 1 residue). I did this
> because
> if I try to define a residue PT with many atoms (possibly all the thousands
> of Pt atoms I need), then in the .top file I get only 1 PT atom in the PT
> residue. I have also added a line corresponding to platinum in
> ffnonbonded.itp (always PT used).
>
> Belonging to different residues, I then try to set a special bond between
> these atoms by editing a specbond.dat file like this:
>
> 1
> PT     PT     1       PT    PT    1       0.29    PT2     PT2
>
> where I have already defined the new residue PT2 with the same
> characteristics as PT.
>

Why? Manual 5.6.7 says renaming the residue is optional. If you do it this
way, how are you going to make more bonds between the newly-named PT2
residues?

Mark


> The fatal error message I get goes like this:
>
> Atom PT in residue PT 314 was not found in rtp entry PT2 with 1 atoms
> while sorting atoms.
>
> Keep in mind that the PT residues in my .pdb file range between 130 and
> 1779.
>
> I guess I am doing in a complicated way and with many evident error
> something that could probably be done in a simpler way. I am sorry for the
> evident error but I am a new user of GROMACS...
>
> Thank you in advance,
>
> Nicola
>
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