Dear Gromacs users,<br><br><br>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.<br>
<br>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. <br><br><span style="font-family: courier new,monospace;">topol.top output__________________________________________</span><br style="font-family: courier new,monospace;">
<br>
<span style="font-family: courier new,monospace;">445 ON 14 ATEM OT5 445 -0.118 16 ; qtot -11.78</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> 446 LP 14 ATEM LP1 446 -0.11 3 ; qtot -11.89</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> 447 Br 14 ATEM LP2 447 0 1.48594e-41 ; qtot -11.89</span><br style="font-family: courier new,monospace;">
<br><br>If i interchange the first two lines of the atomtypes.atp, for LP2 i get atomtype 'C'<br><br><span style="font-family: courier new,monospace;"></span><span style="font-family: courier new,monospace;">C 12.01000 ; sp2 C carbonyl group </span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Br 79.90000 ; bromine</span><br><br>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.<br>
<br>____________________<br><br>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<br>
<br><span style="font-family: courier new,monospace;">pdb2gmx output</span>................<br style="font-family: courier new,monospace;">_____________<br><br><span style="font-family: courier new,monospace;">Opening force field file /home/dsarath/Utilities/share/451//amber99sb.ff/aminoacids.r2b<br>
Opening force field file /home/dsarath/Utilities/share/451//amber99sb.ff/dna.r2b<br>Opening force field file /home/dsarath/Utilities/share/451//amber99sb.ff/rna.r2b<br>Reading Test-5T.pdb...<br>Read 'Great Red Owns Many ACres of Sand', 447 atoms<br>
Analyzing pdb file<br>Splitting PDB chains based on TER records or changing chain id.<br>There are 1 chains and 0 blocks of water and 14 residues with 447 atoms<br><br> chain #res #atoms<br> 1 ' ' 14 447 <br>
All occupancies are one<br></span><span style="font-family: courier new,monospace;">Opening force field file /home/dsarath/Utilities/share/451//amber99sb.ff/atomtypes.atp</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Atomtype 1<br><br style="font-family: courier new,monospace;">-------------------here pdb2gmx hangs</span><br style="font-family: courier new,monospace;"><br><br><br>Best Wishes,<br>
<br><br>Sarath<br><br>________________<br><br>Sarath Chandra Dantu<br>Computational Biomolecular Chemistry<br>Max Planck Institute of Biophysical Chemistry<br>Am Fassberg 11,<br>Gottingen<br>37077<br>Germany<br>