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 <i><a href="http://Dixon.et.al">Dixon.et.al</a> J.Comp.Chem, 18, 1632-1646</i><br>
<br><br><b><span style="font-family: courier new,monospace;">atomtypes.atp entry---------------</span></b><br style="font-family: courier new,monospace;"><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">LP 3.00000 ;</span><br style="font-family: courier new,monospace;">
<br style="font-family: courier new,monospace;"><br style="font-family: courier new,monospace;"><b><span style="font-family: courier new,monospace;">ffnonbonded.itp entry------</span></b><br style="font-family: courier new,monospace;">
<br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">LP 0 3.000 0.0000 A 0.00000e+00 0.00000e+00 ;</span><br style="font-family: courier new,monospace;">
<br>
<br><b><span style="font-family: courier new,monospace;">rna.rtp entry.........</span></b><br><br><span style="font-family: courier new,monospace;">[ ATEM ]</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> [ atoms ]</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> CL CT 0.18734 1</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> HCL HC 0.08035 2</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> CT1 CT -0.07300 3</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> HT11 HC 0.02400 4</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> HT12 HC 0.02400 5</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> CT2 CT -0.07300 6</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> HT21 HC 0.02400 7</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> HT22 HC 0.02400 8</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> CT3 CT 0.18900 9</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> C31 CT -0.08900 10</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> H311 HC 0.02700 11</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> H312 HC 0.02700 12</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> H313 HC 0.02700 13</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> C32 CT -0.08900 14 </span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> H321 HN 0.02700 15</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> H322 HN 0.02700 16</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> H323 HN 0.02700 17</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> CT4 CT 0.18900 18</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> C41 CT -0.08900 19</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> H411 HN 0.02700 20</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> H412 HN 0.02700 21</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> H413 HN 0.02700 22</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> C42 CT -0.08900 23 </span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> H421 HC 0.02700 24</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> H422 HC 0.02700 25</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> H423 HC 0.02700 26</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> NT5 NN 0.03700 27</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> OT5 ON -0.11800 28</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> LP1 LP -0.11000 29</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> LP2 LP -0.11000 30</span><br>
<br><br style="font-family: courier new,monospace;"><br style="font-family: courier new,monospace;"><br style="font-family: courier new,monospace;"><div class="gmail_quote">On Fri, Dec 3, 2010 at 4:40 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Sarath Chandra wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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>
topol.top output__________________________________________<br>
<br>
445 ON 14 ATEM OT5 445 -0.118 16 ; qtot -11.78<br>
446 LP 14 ATEM LP1 446 -0.11 3 ; qtot -11.89<br>
447 Br 14 ATEM LP2 447 0 1.48594e-41 ; qtot -11.89<br>
<br>
<br>
If i interchange the first two lines of the atomtypes.atp, for LP2 i get atomtype 'C'<br>
<br>
C 12.01000 ; sp2 C carbonyl group<br>
Br 79.90000 ; bromine<br>
<br>
</blockquote>
<br></div>
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.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
____________________<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>
pdb2gmx output................<br>
_____________<br>
<br>
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 All occupancies are one<br>
Opening force field file /home/dsarath/Utilities/share/451//amber99sb.ff/atomtypes.atp<br>
Atomtype 1<br>
<br>
-------------------here pdb2gmx hangs<br>
<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>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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