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

[fantaman]

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.

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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