[gmx-users] Problem w.r.t simulation with a Heme containing protein

[Prasanth G, Research Scholar]

Dear all,

I have tried to process the heme containing protein using GROMOS 54a7.
Although I am able to convert the pro.pdb to pro.gro, I am getting a
warning sign, like this,
--------------------------------------
While running
pdb2gmx -f pro.pdb -o pro.gro ....
.
.
.
Before cleaning: 9225 pairs
Before cleaning: 11318 dihedrals
Making cmap torsions...
There are 3062 dihedrals, 3024 impropers, 8613 angles
          9225 pairs,     5884 bonds and     0 virtual sites
Total mass 63413.819 a.m.u.
Total charge -1.000 e
Writing topology
Processing chain 2 'A' (43 atoms, 1 residues)
Warning: Starting residue HEM605 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                  HEM605  HEM605
                   CAB20   CAC27
  HEM605   CAC27   0.815
  HEM605    Fe43   0.582   0.570
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 47 atoms
Chain time...
Making bonds...
Number of bonds was 54, now 54
Generating angles, dihedrals and pairs...
Before cleaning: 15 pairs
Before cleaning: 154 dihedrals
Making cmap torsions...
There are   20 dihedrals,   46 impropers,  102 angles
            15 pairs,       54 bonds and     0 virtual sites
Total mass 614.485 a.m.u.
Total charge -2.000 e
Writing topology
Including chain 1 in system: 5752 atoms 552 residues
Including chain 2 in system: 47 atoms 1 residues
Now there are 5799 atoms and 553 residues
Total mass in system 64028.304 a.m.u.
Total charge in system -3.000 e
-----------------------------------------------------------------
And when I try to add ions using grompp and ions.mdp
i get this...
NOTE 1 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 1795342617
Generated 279 of the 1225 non-bonded parameter combinations

ERROR 1 [file topol_Other_chain_A2.itp, line 162]:
  No default G96Angle types


ERROR 2 [file topol_Other_chain_A2.itp, line 164]:
  No default G96Angle types


ERROR 3 [file topol_Other_chain_A2.itp, line 167]:
  No default G96Angle types


ERROR 4 [file topol_Other_chain_A2.itp, line 169]:
  No default G96Angle types


ERROR 5 [file topol_Other_chain_A2.itp, line 172]:
  No default G96Angle types


ERROR 6 [file topol_Other_chain_A2.itp, line 174]:
  No default G96Angle types


ERROR 7 [file topol_Other_chain_A2.itp, line 177]:
  No default G96Angle types


ERROR 8 [file topol_Other_chain_A2.itp, line 179]:
  No default G96Angle types
--------------------------
Could you please suggest a solution.
Would it help, if i added the following line to residues.dat in $gmx$
---
.
.
IB+    Ion
HEM  Protein


-- 
Regards,
Prasanth.