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

[Nicola Staffolani]

Dear Mark,

thank you very much for your reply.

I do this and then I define the same bonds for PT2 as for PT1 (which of
course sounds redundant, but I had read Manual 5.6.7 and if I do not rename
the residue I get the following message:




*Invalid line 'PT     PT     1       PT     PT    1       0.141' in
specbond.dat0 out of 1 lines of specbond.dat converted successfully*
Keep in mind that I have defined in *top/aminoacids.rtp* both the residues:





*[ PT ]  [ atoms ]  PT       PT    0.00000     0*

*[ PT2 ]*



* [ atoms ]  PT2     PT2     0.00000     0*
Moreover, I have also defined in *top/gromos43a1.ff/atomtypes.atp* both the
PT and the PT2 atom types; in *ffbonded.itp *I have defined:





*; bond-, angle- and dihedraltypes for specbonds:[ bondtypes ]PT2
PT2     2    gb_48*
(having previously defined the stretching bond gb_48); in *ffnonbonded.itp*,
as *[ atomtypes ]*, I have defined both PT and PT2 and then, as said, the
same *c6 *and *c12* for both PT and PT2...

I have just tried to substitute PT for PT2 in ffbonded.itp and to remove
the renaming of the residues in specboond.dat, but I get the same message,
i.e.




*Invalid line 'PT     PT     1       PT     PT    1       0.141' in
specbond.dat0 out of 1 lines of specbond.dat converted successfully*
My version of gromacs is the 4.6.5...



On Wed, Apr 23, 2014 at 5:29 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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
> >
> > --
> > View this message in context:
> >
> http://gromacs.5086.x6.nabble.com/Special-bond-between-metallic-layers-protein-tp5016022.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
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-- 
Nicola Staffolani PhD
Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics>
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffolani at unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36