Dear Mark,<br>I think that i couldn't explain my problem clearly, however i have changed my .rtp but i don't know how should be my .hdb file.<br><br>a) The structure of <b><u>BOC</u></b> is: <b>-<span style="color: rgb(102, 0, 0);">C</span><span style="color: rgb(102, 102, 0);">O</span>-<span style="color: rgb(102, 0, 0);">C</span><span style="color: rgb(102, 51, 102);">H2</span>-<span style="color: rgb(102, 0, 0);">C</span><span style="color: rgb(102, 51, 102);">H</span>(<span style="color: rgb(102, 0, 0);">C6</span><span style="color: rgb(102, 51, 102);">H5</span><span style="color: rgb(51, 51, 0);">Cl</span>)-<span style="color: rgb(102, 0, 0);">C</span><span style="color: rgb(102, 51, 102);">H2</span>-<span style="color: rgb(0, 0, 102);">N</span><span style="color: rgb(102, 51, 102);">H</span>-</b><br>
b) This is the new charges:<br><span style="background-color: rgb(255, 204, 153);">[ BOC ]</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> [ atoms ]</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> N opls_238 -0.500 1 </span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> H opls_241 0.300 1</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CA opls_224B 0.080 1</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> HA1 opls_140 0.060 1</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HA2 opls_140 0.060 1</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> CB opls_149 0.055 2</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HB opls_140 0.060 2</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> CG1 opls_145 -0.115 2</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CD1 opls_145 -0.115 3</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> HD1 opls_146 0.115 3</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CD2 opls_145 -0.115 4</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> HD2 opls_146 0.115 4</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CE1 opls_145 -0.115 5</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> HE1 opls_146 0.115 5</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CE2 opls_145 -0.115 6</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> HE2 opls_146 0.115 6 </span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CZ opls_145 1.000 7</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> Cl opls_264 -1.000 7</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CG2 opls_071 -0.120 8</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> HG1 opls_140 0.060 8</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HG2 opls_140 0.060 8</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> C opls_235 0.700 9</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> O opls_236 -0.700 9</span><br>c) charge for CG1 in PHE (in OPLS .rtp) is negative, too.<br>d) Would you explain for me that what is wrong in my atom types?<br>
e) As you see in the error, at first there are 63 residues (like my pdb) but when when it adds COO- and NH3+ there are 69 residues! it should add only one "O" (for COO-) and two "H"s for (NH3+) i think.<br>
<br><span style="background-color: rgb(204, 255, 255);">There are 1 chains and 0 blocks of water and <span style="background-color: rgb(255, 204, 204);">3</span> residues with <span style="background-color: rgb(255, 204, 204);">63</span> atoms</span><br style="background-color: rgb(204, 255, 255);">
<br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);"> chain #res #atoms</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);"> 1 ' ' 3 63 </span><br style="background-color: rgb(204, 255, 255);">
<br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">All occupancy fields zero. This is probably not an X-Ray structure</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Opening library file /usr/share/gromacs/top/ffoplsaa.atp</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Atomtype 1</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Reading residue database... (ffoplsaa)</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Opening library file /usr/share/gromacs/top/ffoplsaa.rtp</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Residue 57</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Sorting it all out...</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Opening library file /usr/share/gromacs/top/ffoplsaa.hdb</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb</span><br style="background-color: rgb(204, 255, 255);"><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Back Off! I just backed up topol.top to ./#topol.top.3#</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Processing chain 1 (63 atoms, 3 residues)</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">There are 3 donors and 3 acceptors</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">There are 4 hydrogen bonds</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Checking for duplicate atoms....</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Opening library file /usr/share/gromacs/top/specbond.dat</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">7 out of 7 lines of specbond.dat converted succesfully</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">N-terminus: NH3+</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">C-terminus: COO-</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(255, 204, 204);">Now there are 3 residues with 69 atoms</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Making bonds...</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Warning: Long Bond (53-54 = 0.334847 nm)</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Warning: Long Bond (53-56 = 0.334912 nm)</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Warning: Long Bond (64-65 = 0.271173 nm)</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Warning: Long Bond (64-66 = 0.347808 nm)</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Warning: Long Bond (64-67 = 0.31288 nm)</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Opening library file /usr/share/gromacs/top/aminoacids.dat</span><br style="background-color: rgb(204, 255, 255);">
<br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">-------------------------------------------------------</span><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Program pdb2gmx, VERSION 4.0.7</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Source code file: ../../../../src/kernel/add_par.c, line: 233</span><br style="background-color: rgb(204, 255, 255);"><br style="background-color: rgb(204, 255, 255);"><span style="background-color: rgb(204, 255, 255);">Fatal error:</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Atom HB1 not found in rtp database in residue BOC, it looks a bit like HB</span><br> <br><br> <br>