<div>hello Tsjerk:</div>
<div>Thank you very much! That does work, but another problem appeared as following:</div>
<div>creating statusfile for 1 node...<br>checking input for internal consistency...<br>calling /lib/cpp...<br>processing topology...<br>Generated 1284 of the 1485 non-bonded parameter combinations<br>WARNING 1 [file "
com.top", line 519]:<br> Too few parameters on line (source file toppush.c, line 932)<br>WARNING 2 [file "com.top", line 520]:<br> Too few parameters on line (source file toppush.c, line 932)<br>processing coordinates...
<br>Fatal error: number of coordinates in coordinate file (com_wat.gro, 2837)<br> does not match topology (com.top, 0)<br>actually i only perform the following:</div>
<div>
<p class="MsoNormal" style="MARGIN: 0pt"><span lang="EN-US"><font face="Times New Roman">editconf 每bt cubic 每f com.gro 每o com_box.gro 每d 0.8</font></span></p>
<p class="MsoNormal" style="MARGIN: 0pt"><span lang="EN-US"><font face="Times New Roman">genbox 每cp com_box.gro 每cs spc216.gro 每p com.top 每o com_wat.gro</font></span></p>
<p class="MsoNormal" style="MARGIN: 0pt"><span lang="EN-US"><font face="Times New Roman">grompp 每f em.mdp 每c com_wat.gro 每p com.top 每o com_em.tpr</font></span></p>
<p class="MsoNormal" style="MARGIN: 0pt"><span lang="EN-US"><font face="Times New Roman">and my com.gro file was as following:</font></span></p>
<p class="MsoNormal" style="MARGIN: 0pt"><span lang="EN-US">PRODRG COORDS<br> 80<br> 1DRG CAH 1 -0.832 -0.624 -0.960<br> 1DRG CAS 2 -0.746 -0.538 -0.867<br> 1DRG CAT 3 -0.710 -0.410 -
0.942<br> 1DRG CBI 4 -0.621 -0.618 -0.830<br> 1DRG CCF 5 -0.555 -0.585 -0.694<br> 1DRG CCG 6 -0.647 -0.615 -0.575<br> 1DRG OCU 7 -0.750 -0.706 -0.587<br> 1DRG OBJ 8 -
0.629 -0.560 -0.467<br> 1DRG NCE 9 -0.506 -0.445 -0.688<br> 1DRG HAG 10 -0.556 -0.385 -0.626<br> 1DRG CCD 11 -0.401 -0.405 -0.761<br> 1DRG OBH 12 -0.345 -0.480 -0.843<br> 1DRG CCC 13 -
0.347 -0.263 -0.745<br> 1DRG CBG 14 -0.439 -0.163 -0.817<br> 1DRG CAQ 15 -0.381 -0.024 -0.851<br> 1DRG CAG 16 -0.248 -0.030 -0.926<br> 1DRG CAR 17 -0.363 0.065 -0.727<br> 1DRG NCB 18 -
0.326 -0.229 -0.603<br> 1DRG HAF 19 -0.405 -0.241 -0.543<br> 1DRG CCA 20 -0.206 -0.185 -0.563<br> 1DRG OBF 21 -0.113 -0.159 -0.640<br> 1DRG CBZ 22 -0.187 -0.168 -0.413<br> 1DRG CBE 23 -
0.126 -0.302 -0.370<br> 1DRG CAO 24 -0.241 -0.394 -0.332<br> 1DRG OAF 25 -0.338 -0.339 -0.274<br> 1DRG OAP 26 -0.230 -0.514 -0.360<br> 1DRG NBY 27 -0.106 -0.046 -0.388<br> 1DRG HAE 28 -
0.084 0.000 -0.473<br> 1DRG CBX 29 -0.062 0.009 -0.273<br> 1DRG OBD 30 -0.012 0.122 -0.272<br> 1DRG CBW 31 -0.067 -0.063 -0.137<br> 1DRG CBC 32 0.078 -0.071 -0.084<br> 1DRG CAN 33
0.164 -0.170 -0.163<br> 1DRG CBB 34 0.089 -0.114 0.063<br> 1DRG NBV 35 -0.154 0.013 -0.045<br> 1DRG HAD 36 -0.131 0.111 -0.043<br> 1DRG CBU 37 -0.254 -0.032 0.032<br> 1DRG OBA 38 -
0.296 0.039 0.123<br> 1DRG CBT 39 -0.315 -0.174 0.014<br> 1DRG CAZ 40 -0.241 -0.277 0.099<br> 1DRG CAL 41 -0.206 -0.403 0.018<br> 1DRG CAE 42 -0.326 -0.495 -0.002<br> 1DRG CAM 43 -
0.094 -0.481 0.088<br> 1DRG NBS 44 -0.452 -0.166 0.069<br> 1DRG HAC 45 -0.449 -0.181 0.167<br> 1DRG CBR 46 -0.575 -0.144 0.017<br> 1DRG OAY 47 -0.666 -0.135 0.100<br> 1DRG CBQ 48 -
0.618 -0.126 -0.131<br> 1DRG CAX 49 -0.520 -0.056 -0.228<br> 1DRG CAJ 50 -0.533 0.096 -0.242<br> 1DRG CAD 51 -0.499 0.173 -0.114<br> 1DRG CAK 52 -0.673 0.137 -0.289<br> 1DRG NBP 53 -
0.666 -0.245 -0.201<br> 1DRG HAB 54 -0.595 -0.302 -0.244<br> 1DRG C 55 -0.797 -0.274 -0.207<br> 1DRG O 56 -0.872 -0.267 -0.109<br> 1DRG CA 57 -0.856 -0.322 -0.340<br> 1DRG CB 58 -
0.777 -0.276 -0.463<br> 1DRG CG 59 -0.821 -0.140 -0.516<br> 1DRG CD 60 -0.725 -0.105 -0.629<br> 1DRG OE2 61 -0.635 -0.023 -0.602<br> 1DRG OE1 62 -0.741 -0.164 -0.738<br> 1DRG N 63 -
0.871 -0.467 -0.358<br> 1DRG HAA 64 -0.795 -0.522 -0.325<br> 1DRG CBL 65 -0.981 -0.519 -0.414<br> 1DRG OAU 66 -1.093 -0.467 -0.410<br> 1DRG CBK 67 -0.968 -0.654 -0.484<br> 1DRG CCT 68 -
0.833 -0.725 -0.469<br> 1DRG CCS 69 -0.860 -0.875 -0.449<br> 1DRG CCR 70 -0.929 -0.913 -0.316<br> 1DRG CCQ 71 -0.842 -0.888 -0.192<br> 1DRG CCP 72 -0.880 -0.760 -0.116<br> 1DRG CCO 73 -
0.763 -0.714 -0.029<br> 1DRG CCN 74 -0.792 -0.577 0.034<br> 1DRG CCM 75 -0.676 -0.523 0.119<br> 1DRG CCL 76 -0.670 -0.578 0.263<br> 1DRG CCK 77 -0.593 -0.710 0.282<br> 1DRG CCJ 78 -
0.440 -0.698 0.279<br> 1DRG CCI 79 -0.385 -0.625 0.402<br> 1DRG CCH 80 -0.232 -0.622 0.401<br> 1.51200 1.51200 1.51200<br>Thank you very much!</span></p></div>