[gmx-users] pdb2gmx and atomtype.atp
Justin A. Lemkul
jalemkul at vt.edu
Fri Dec 3 16:40:53 CET 2010
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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