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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