[gmx-users] pdb2gmx and atomtype.atp

Sarath Chandra sarathchandradantu at gmail.com
Fri Dec 3 16:51:12 CET 2010


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 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 <jalemkul at 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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