Please file a bugzilla, uploading all of the input files needed to reproduce the problem. It appears that you can cause LP2 to be assigned an LP type if it is the first line in atomtypes.atp, but the mass and charge are still nonsense. Certainly you can manually modify the topology to fix this problem, but it is definitely an important bug worth fixing.

-Justin

Sarath Chandra wrote:
Gromacs version used was 4.5.3. I have added the new atomtype LP in the atomtype.atp and I have also defined the nonbonded+bonded interactions for LP. Parameters for LP were obtained from /Dixon.et.al <http://Dixon.et.al> J.Comp.Chem, 18, 1632-1646/


*atomtypes.atp entry---------------*

LP                 3.00000      ;


*ffnonbonded.itp entry------*

LP           0      3.000    0.0000  A   0.00000e+00  0.00000e+00 ;


*rna.rtp entry.........*

[ ATEM ]
 [ atoms ]
    CL    CT            0.18734     1
   HCL    HC            0.08035     2
   CT1    CT           -0.07300     3
  HT11    HC            0.02400     4
  HT12    HC            0.02400     5
   CT2    CT           -0.07300     6
  HT21    HC            0.02400     7
  HT22    HC            0.02400     8
   CT3    CT            0.18900     9
   C31    CT           -0.08900    10
  H311    HC            0.02700    11
  H312    HC            0.02700    12
  H313    HC            0.02700    13
   C32    CT           -0.08900    14
  H321    HN            0.02700    15
  H322    HN            0.02700    16
  H323    HN            0.02700    17
   CT4    CT            0.18900    18
   C41    CT           -0.08900    19
  H411    HN            0.02700    20
  H412    HN            0.02700    21
  H413    HN            0.02700    22
   C42    CT           -0.08900    23
  H421    HC            0.02700    24
  H422    HC            0.02700    25
  H423    HC            0.02700    26
   NT5    NN            0.03700    27
   OT5    ON           -0.11800    28
   LP1    LP           -0.11000    29
   LP2    LP           -0.11000    30




On Fri, Dec 3, 2010 at 4:40 PM, Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> wrote:



    Sarath Chandra wrote:

        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


    This indicates to me that pdb2gmx is failing to find an appropriate
    atom type and is instead simply assigning the first type it comes
    to, yielding undefined charges and masses.


        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.


    There isn't an "LP" type by default in atomtypes.atp for
    amber99sb.ff; have you added it?  What's in your .rtp file?  You
    haven't shown us any relevant input, so it's impossible to diagnose
    whether this is a Gromacs problem or just something you've overlooked.

    -Justin


        ____________________

        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


-- ========================================

    Justin A. Lemkul
    Ph.D. Candidate
    ICTAS Doctoral Scholar
    MILES-IGERT Trainee
    Department of Biochemistry
    Virginia Tech
    Blacksburg, VA
    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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