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 <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 | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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