[gmx-users] pdb2gmx and atomtype.atp

[Sarath Chandra]

Dear Gromacs users,


I have a nitroxide radical with lone pairs on oxygen which has to be
attached to Adenine of a RNA. I have the forcefiled for the nitroxide
radical and as well as i have obtained the charges for the link atoms using
resp. I use specbond.dat to make the link between the nucleotide and the
radical molecule and all of that goes well. The problem comes in the
topol.top file. Lonepair on oxygen has an atom type LP and I have two lone
pairs LP1 and LP2.

The atomtype charge and mass for LP1 are assigned properly but for the LP2
atomtype is that of 'Br' and charge is 0 mass is just weird.

topol.top output__________________________________________

 445         ON     14   ATEM    OT5    445     -0.118         16   ; qtot
-11.78
 446         LP     14   ATEM    LP1    446      -0.11          3   ; qtot
-11.89
 447         Br     14   ATEM    LP2    447          0 1.48594e-41   ; qtot
-11.89


If i interchange the first two lines of the atomtypes.atp, for LP2 i get
atomtype 'C'

C                 12.01000    ; sp2 C carbonyl group
Br                79.90000    ; bromine

If there was a problem with the forcefield files the error in assigning
atomtypes should happen for both LP1 and LP2. I have played with the atom
names using LPx and LPy, the error repeats with LPy and I also changed the
atom lines order in the pdb file. I can simply correct the atomtype, mass,
charge and my simulation works well. No problems with grompp either. I have
checked the line spacings and they are all fine. I was just wondering if
there is something I have overlooked or if it was a bug.

____________________

A small second issue to report that if you introduce a blank line (either
for fun or by mistake) at the end of the atomtypes.atp file, pdb2gmx hangs
and stays like that until you kill it

pdb2gmx output................
_____________

Opening force field file
/home/dsarath/Utilities/share/451//amber99sb.ff/aminoacids.r2b
Opening force field file
/home/dsarath/Utilities/share/451//amber99sb.ff/dna.r2b
Opening force field file
/home/dsarath/Utilities/share/451//amber99sb.ff/rna.r2b
Reading Test-5T.pdb...
Read 'Great Red Owns Many ACres of Sand', 447 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 14 residues with 447 atoms

  chain  #res #atoms
  1 ' '    14    447
All occupancies are one
Opening force field file
/home/dsarath/Utilities/share/451//amber99sb.ff/atomtypes.atp
Atomtype 1

-------------------here pdb2gmx hangs



Best Wishes,


Sarath

________________

Sarath Chandra Dantu
Computational Biomolecular Chemistry
Max Planck Institute of Biophysical Chemistry
Am Fassberg 11,
Gottingen
37077
Germany
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