Thank you very much, Mark!<br>Now i have errors from my .top file after grompp command.<br>The question is that why in pdb2gmx, editconf ,genbox and make_ndx steps i don't see these errors:<br><br><span style="background-color: rgb(255, 204, 153);">...</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">processing topology...</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">Opening library file /usr/share/gromacs/top/ffoplsaa.itp</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Opening library file /usr/share/gromacs/top/ffoplsaanb.itp</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">Opening library file /usr/share/gromacs/top/ffoplsaabon.itp</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Generated 332520 of the 332520 non-bonded parameter combinations</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">Generating 1-4 interactions: fudge = 0.5</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Generated 332520 of the 332520 1-4 parameter combinations</span><br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">ERROR 1 [file topol.top, line 412]:</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> No default Angle types</span><br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">ERROR 2 [file topol.top, line 567]:</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> No default Ryckaert-Bell. types</span><br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">ERROR 3 [file topol.top, line 570]:</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> No default Ryckaert-Bell. types</span><br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">ERROR 4 [file topol.top, line 573]:</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> No default Ryckaert-Bell. types</span><br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">ERROR 5 [file topol.top, line 580]:</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> No default Ryckaert-Bell. types</span><br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">ERROR 6 [file topol.top, line 581]:</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> No default Ryckaert-Bell. types</span><br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">ERROR 7 [file topol.top, line 582]:</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> No default Ryckaert-Bell. types</span><br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">Opening library file /usr/share/gromacs/top/spc.itp</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Opening library file /usr/share/gromacs/top/ions.itp</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">Excluding 3 bonded neighbours molecule type 'Protein'</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Excluding 2 bonded neighbours molecule type 'SOL'</span><br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">NOTE 1 [file topol.top, line 664]:</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> System has non-zero total charge: 6.000000e-02</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);"> </span><br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">processing coordinates...</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">double-checking input for internal consistency...</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">renumbering atomtypes...</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">converting bonded parameters...</span><br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">There was 1 note</span><br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">-------------------------------------------------------</span><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">Program grompp, VERSION 4.0.7</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Source code file: ../../../../src/kernel/grompp.c, line: 986</span><br style="background-color: rgb(255, 204, 153);"><br style="background-color: rgb(255, 204, 153);"><span style="background-color: rgb(255, 204, 153);">Fatal error:</span><br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">There were 7 errors in input file(s)</span><br><br><b>topol.top:</b><br>...<br> <span style="background-color: rgb(255, 204, 153);">43</span> opls_238 3 BOC <span style="background-color: rgb(255, 204, 153);">N</span> 17 -0.5 14.0067 ; qtot 0.5<br>
44 opls_241 3 BOC H 17 0.3 1.008 ; qtot 0.8<br> <span style="background-color: rgb(255, 204, 153);">45</span> opls_283 3 BOC <span style="background-color: rgb(255, 204, 153);">CA</span> 17 0.04 12.011 ; qtot 0.84<br>
<span style="background-color: rgb(255, 204, 153);">46</span> opls_140 3 BOC <span style="background-color: rgb(255, 204, 153);">HA1</span> 17 0.06 1.008 ; qtot 0.9<br> <span style="background-color: rgb(255, 204, 153);">47</span> opls_140 3 BOC <span style="background-color: rgb(255, 204, 153);"> HA2</span> 17 0.06 1.008 ; qtot 0.96<br>
<span style="background-color: rgb(255, 204, 153);">48</span> opls_149 3 BOC <span style="background-color: rgb(255, 204, 153);">CB</span> 18 0.055 12.011 ; qtot 1.015<br> 49 opls_140 3 BOC HB 18 0.06 1.008 ; qtot 1.075<br>
50 opls_145 3 BOC CG1 18 -0.115 12.011 ; qtot 0.96<br> 51 opls_145 3 BOC CD1 19 -0.115 12.011 ; qtot 0.845<br> 52 opls_146 3 BOC HD1 19 0.115 1.008 ; qtot 0.96<br>
53 opls_145 3 BOC CD2 20 -0.115 12.011 ; qtot 0.845<br> 54 opls_146 3 BOC HD2 20 0.115 1.008 ; qtot 0.96<br> 55 opls_145 3 BOC CE1 21 -0.115 12.011 ; qtot 0.845<br>
56 opls_146 3 BOC HE1 21 0.115 1.008 ; qtot 0.96<br> 57 opls_145 3 BOC CE2 22 -0.115 12.011 ; qtot 0.845<br> 58 opls_146 3 BOC HE2 22 0.115 1.008 ; qtot 0.96<br>
59 opls_145 3 BOC CZ 23 1 12.011 ; qtot 1.96<br> 60 opls_264 3 BOC Cl 23 -1 35.453 ; qtot 0.96<br> <span style="background-color: rgb(255, 204, 153);">61</span> opls_224B 3 BOC <span style="background-color: rgb(255, 204, 153);">CG2</span> 24 -0.12 12.011 ; qtot 0.84<br>
<span style="background-color: rgb(255, 204, 153);">62</span> opls_140 3 BOC <span style="background-color: rgb(255, 204, 153);">HG1</span> 24 0.06 1.008 ; qtot 0.9<br> <span style="background-color: rgb(255, 204, 153);">63</span> opls_140 3 BOC <span style="background-color: rgb(255, 204, 153);">HG2</span> 24 0.06 1.008 ; qtot 0.96<br>
<span style="background-color: rgb(255, 204, 153);">64</span> opls_271 3 BOC <span style="background-color: rgb(255, 204, 153);"> C</span> 25 0.7 12.011 ; qtot 1.66<br> 65 opls_272 3 BOC O1 25 -0.8 15.9994 ; qtot 0.86<br>
66 opls_272 3 BOC O2 25 -0.8 15.9994 ; qtot 0.06<br>...<br>[ angles ]<br>...<br><span style="background-color: rgb(255, 204, 204);">line 412</span>: 45 48 61 1<br>...<br>[ dihedrals ]<br>
...<br><span style="background-color: rgb(255, 204, 204);">line 567</span>: 43 45 48 61 3 <br>...<br><span style="background-color: rgb(255, 204, 204);">line 570</span>: 46 45 48 61 3 <br>...<br>
<span style="background-color: rgb(255, 204, 204);">line 573</span>: 47 45 48 61 3 <br>...<br><span style="background-color: rgb(255, 204, 204);">line 580</span>: 45 48 61 62 3 <br><span style="background-color: rgb(255, 204, 204);">line 581</span>: 45 48 61 63 3 <br>
<span style="background-color: rgb(255, 204, 204);">line 582</span>: 45 48 61 64 3 <br>...<br><br>it seems that "45 48 61" is the problem. CA CB CG2 <br>Where i should define angle type for it?<br>
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