<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div class="tripane message content"> <div class="msg-body inner undoreset" style=""><div id="yiv1508721392"><div><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt;"><div>Hello</div><div>after use of grompp I got the following errors:</div><div><br></div><div>ERROR 1 [file topol.top, line 172]:<br> No default Angle types<br><br>this error repeats<br><br>ERROR 38 [file topol.top, line 233]:<br> No default Improper Dih. types<br><br>this error repeats also<br><br>Excluding 3 bonded neighbours molecule type 'Isoalloxazin'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br><br>NOTE 1 [file topol.top, line 278]:<br> System has non-zero total charge: 0.000400<br> Total charge should normally be an integer. <br><br>There was 1
note<br>-------------------------------------------------------<br>Program grompp, VERSION 4.5.5<br>Source code file: /home/me/src/gromacs-4.5.5/src/kernel/grompp.c, line: 1372<br><br>Fatal error:<br>There were 55 errors in input file(s)</div><div><br></div><div>I give you my topology file. Could you please tell me what there
is false? <br></div><div><br>#include "./charmm27_local.ff/forcefield.itp"<br><br>[ moleculetype ]<br>; Name nrexcl<br>Isoalloxazin 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br>; residue 1 ISO rtp ISO q 0.0<br> 1 NN3A 1
ISO N1 1 -0.6519 14.007 ; qtot -0.6519<br> 2 CN1A 1 ISO C2 2 0.7481 12.011 ; qtot 0.0962<br> 3 ON1 1 ISO O2 3 -0.7371 15.9994 ; qtot -0.6409<br> 4 NN2U 1 ISO N3 4 -0.4064 14.007 ; qtot
-1.047<br> 5 HN2 1 ISO H3 5 0.358 1.008 ; qtot -0.6893<br> 6 CN1B 1 ISO C4 6 0.4925 12.011 ; qtot -0.1968<br> 7 ON1 1 ISO O4 7 -0.6824 15.9994 ; qtot -0.8792<br> 8 CN5B 1
ISO C4A 8 0.0224 12.011 ; qtot -0.8568<br> 9 NN3A 1 ISO N5 9 -0.2742 14.007 ; qtot -1.131<br> 10 CPTB 1 ISO C5A 10 0.1797 12.011 ; qtot -0.9513<br> 11 CA1 1 ISO C6 11 -0.2904 12.011 ; qtot -1.242<br>
12 HP 1 ISO H6 12 0.3012 1.008 ; qtot -0.9405<br> 13 CA2 1 ISO C7 13 0.1958 12.011 ; qtot -0.7447<br> 14 CA3 1 ISO C8 14 0.07 12.011 ; qtot -0.6747<br> 15 CA4 1 ISO
C9 15 -0.0292 12.011 ; qtot -0.7039<br> 16 HP 1 ISO H9 16 0.1949 1.008 ; qtot -0.509<br> 17 CPTA 1 ISO C9A 17 -0.1901 12.011 ; qtot -0.6991<br> 18 NN2G 1 ISO N10 18 0.273 14.007 ; qtot -0.4261<br> 19
CN5A 1 ISO C0A 19 0.2618 12.011 ; qtot -0.1643<br> 20 CT3 1 ISO C7M 20 -0.3701 12.011 ; qtot -0.5344<br> 21 HAI 1 ISO H7A 21 0.1234 1.008 ; qtot -0.411<br> 22 HAI 1 ISO H7B 22 0.1234
1.008 ; qtot -0.2876<br> 23 HAI 1 ISO H7C 23 0.1234 1.008 ; qtot -0.1642<br> 24 CT3 1 ISO C8M 24 -0.3645 12.011 ; qtot -0.5287<br> 25 HAI 1 ISO H8A 25 0.1215 1.008 ; qtot -0.4072<br> 26 HAI 1
ISO H8B 26 0.1215 1.008 ; qtot -0.2857<br> 27 HAI 1 ISO H8C 27 0.1215 1.008 ; qtot -0.1642<br> 28 CT3 1 ISO C0M 28 -0.3952 12.011 ; qtot -0.5594<br> 29 HAI 1 ISO H0A 29 0.1318 1.008 ; qtot -0.4276<br>
30 HAI 1 ISO H0B 30 0.1318 1.008 ; qtot -0.2958<br> 31 HAI 1 ISO H0C 31 0.1318 1.008 ; qtot -0.164<br> 32 HP 1 ISO H5 32 0.1644 1.008 ; qtot 0.0004<br><br>[ bonds ]<br>; ai aj funct
c0 c1 c2 c3<br> 1 2 1 287.0 1.382<br> 1 19 1 381.2 1.320<br> 2 3 1 691.5 1.229<br> 2 4 1 176.0 1.429<br> 4 5 1 459.8 1.022<br> 4 6
1 281.2 1.384<br> 6 7 1 667.7 1.244<br> 6 8 1 262.6 1.450<br> 8 9 1 355.8 1.365<br> 8 19 1 362.5 1.416<br> 9 10 1 297.3 1.379<br> 9 32 1 459.3 1.027<br> 10 11 1
362.7 1.402<br> 10 17 1 322.8 1.424<br> 11 12 1 375.5 1.094<br> 11 13 1 341.7 1.395<br> 13 14 1 312.9 1.417<br> 13 20 1 265.1 1.507<br> 14 15 1 353.5 1.402<br> 14 24 1 266.9 1.507<br> 15
16 1 382.1 1.090<br> 15 17 1 334.8 1.402<br> 17 18 1 285.9 1.402<br> 18 19 1 270.1 1.404<br> 18 28 1 260.2 1.463<br> 20 21 1 356.5 1.100<br> 20 22 1 356.5 1.100<br> 20 23 1 356.5
1.100<br> 24 25 1 356.5 1.100<br> 24 26 1 356.5 1.100<br> 24 27 1 356.5 1.100<br> 28 29 1 356.5 1.100<br> 28 30 1 356.5 1.100<br> 28 31 1 356.5 1.100<br><br>[ pairs ]<br>; ai aj funct c0
c1 c2 c3<br> 1 5 1 <br> 1 6 1 <br> 1 9 1 <br> 1 17 1 <br> 1 28 1 <br> 2 7 1 <br> 2 8 1 <br> 2 18 1 <br> 3 5 1 <br> 3 6 1 <br> 3 19 1
<br> 4 9 1 <br> 4 19 1 <br> 5 7 1 <br> 5 8 1 <br> 6 10 1 <br> 6 18 1 <br> 6 32 1 <br> 7 9 1 <br> 7 19 1 <br> 8 11 1 <br> 8 17 1 <br> 8 28 1 <br> 9 12 1
<br> 9 13 1 <br> 9 15 1 <br> 9 18 1 <br> 10 14 1 <br> 10 16 1 <br> 10 19 1 <br> 10 20 1 <br> 10 28 1 <br> 11 15 1 <br> 11 18 1 <br> 11 21 1 <br> 11 22 1 <br> 11 23 1 <br> 11 24 1
<br> 11 32 1 <br> 12 14 1 <br> 12 17 1 <br> 12 20 1 <br> 13 16 1 <br> 13 17 1 <br> 13 25 1 <br> 13 26 1 <br> 13 27 1 <br> 14 18 1 <br> 14 21 1 <br> 14 22 1 <br> 14 23 1 <br> 15 19 1 <br>
15 20 1 <br> 15 25 1 <br> 15 26 1 <br> 15 27 1 <br> 15 28 1 <br> 16 18 1 <br> 16 24 1 <br> 17 24 1 <br> 17 29 1 <br> 17 30 1 <br> 17 31 1 <br> 17 32 1 <br> 19 29 1 <br> 19 30 1 <br> 19
31 1 <br> 19 32 1 <br> 20 24 1 <br><br>[ angles ]<br>; ai aj ak funct c0 c1 c2 c3<br> 2 1 19 1 <br> 1 2 3 1 250.00 123.75<br> 1 2 4 1 230.00 117.47<br>
3 2 4 1 <br> 2 4 5 1 105.00 115.95<br> 2 4 6 1 90.00 126.44<br> 5 4 6 1 <br> 4 6 7 1 225.00 124.66<br> 4 6 8 1 100.00 112.38<br> 7 6 8 1 <br> 6
8 9 1 110.00 118.06<br> 6 8 19 1 <br> 9 8 19 1 <br> 8 9 10 1 250.00 122.10<br> 8 9 32 1 53.75 115.50<br> 10 9 32 1 <br> 9 10 11 1 80.00 121.96<br> 9 10 17 1 <br>
11 10 17 1 <br> 10 11 12 1 53.75 118.46<br> 10 11 13 1 250.00 121.72<br> 12 11 13 1 <br> 11 13 14 1 75.00 118.68<br> 11 13 20 1 70.00 120.23<br> 14 13 20 1 <br> 13 14 15 1 77.00
119.56<br> 13 14 24 1 70.50 120.72<br> 15 14 24 1 <br> 14 15 16 1 75.00 118.45<br> 14 15 17 1 230.00 122.24<br> 16 15 17 1 <br> 10 17 15 1 <br> 10 17 18 1 <br> 15 17 18 1 52.25 122.22<br> 17
18 19 1 350.00 121.14<br> 17 18 28 1 81.25 120.07<br> 19 18 28 1 <br> 1 19 8 1 <br> 1 19 18 1 <br> 8 19 18 1 <br> 13 20 21 1 <br> 13 20 22 1 <br> 13 20 23 1 <br> 21 20
22 1 <br> 21 20 23 1 <br> 22 20 23 1 <br> 14 24 25 1 <br> 14 24 26 1 <br> 14 24 27 1 <br> 25 24 26 1 <br> 25 24 27 1 <br> 26 24 27 1 <br> 18 28 29 1 <br> 18 28 30 1 <br> 18 28
31 1 <br> 29 28 30 1 <br> 29 28 31 1 <br> 30 28 31 1 <br><br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3 c4 c5<br> 19 1 2 3 2 <br>
2 1 19 8 2 <br> 1 2 4 6 2 <br> 2 4 6 7 2 <br> 4 6 8 9 2 <br> 6 8 9 10 2 <br> 6 8 19 1 2 <br> 8 9 10 11 2 <br> 9 10 11 13
2 <br> 9 10 17 15 2 <br> 10 11 13 14 2 <br> 11 13 14 15 2 <br> 11 13 20 21 2 <br> 13 14 15 17 2 <br> 13 14 24 25 2 <br> 14 15 17 10 2 <br> 10 17 18 19 2 <br> 17 18 19
1 2 <br> 17 18 28 29 2 <br><br>; Include Position restraint file<br>#ifdef POSRES<br>#include "posre.itp"<br>#endif<br><br>; Include water topology<br>#include "./charmm27_local.ff/tip3p.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>#endif<br><br>; Include topology for ions<br>#include "./charmm27_local.ff/ions.itp"<br><br>[ system ]<br>; Name<br>Protein in water<br><br>[ molecules ]<br>; Compound
#mols<br>Isoalloxazin 1<br>SOL 606<br><br></div></div></div></div> </div> </div></div></body></html>