[gmx-users] pdb2gmx and atomtype.atp

[Justin A. Lemkul]

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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