Dear users,<br><br>Before energy minimization step , I performed the preprosessing step using grompp .<br>However, there are two note that :<br><br><b><u>NOTE 1 [file topol.top, line 52]:</u></b><br> System has non-zero total charge: -1.500000e+01<br>
<br><u><b>NOTE 2 [file topol.top]:</b></u><br> The largest charge group contains 11 atoms.<br> Since atoms only see each other when the centers of geometry of the charge<br> groups they belong to are within the cut-off distance, too large charge<br>
groups can lead to serious cut-off artifacts.<br> For efficiency and accuracy, charge group should consist of a few atoms.<br> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><b><br>PS: </b>TRS and EDO are not aminoacid<b><br>
<br><u>TRS.itp:</u></b><br>
..<br>[ moleculetype ]<br>; Name nrexcl<br>TRS 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 OA 1 TRS O1 1 -0.119 15.9994 <br> 2 H 1 TRS H13 1 0.032 1.0080 <br>
3 CH2 1 TRS C1 1 0.087 14.0270 <br> 4 CCl4 1 TRS C 2 0.055 12.0110 <br> 5 CH2 1 TRS C3 2 0.049 14.0270 <br> 6 OA 1 TRS O3 2 -0.205 15.9994 <br>
7 H 1 TRS H33 2 0.019 1.0080 <br> 8 NL 1 TRS N 2 0.206 14.0067 <br> 9 H 1 TRS H2 2 0.004 1.0080 <br> 10 H 1 TRS H3 2 0.004 1.0080 <br>
11 H 1 TRS H1 2 0.004 1.0080 <br> 12 CH2 1 TRS C2 2 0.050 14.0270 <br> 13 OA 1 TRS O2 2 -0.205 15.9994 <br> 14 H 1 TRS H23 2 0.019 1.0080 <br>
...<br><br><u><b>EDO.itp</b></u><br>...<br>[ moleculetype ]<br>; Name nrexcl<br>EDO 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 OA 1 EDO OAB 1 -0.111 15.9994 <br>
2 H 1 EDO HAE 1 0.031 1.0080 <br> 3 CH2 1 EDO CAA 1 0.080 14.0270 <br> 4 CH2 1 EDO CAC 1 0.080 14.0270 <br> 5 OA 1 EDO OAD 1 -0.111 15.9994 <br>
6 H 1 EDO HAF 1 0.031 1.0080 <br>...<br><u><b><br>topol.top:</b></u><br>..<br>; Include water topology<br>#include "gromos43a1.ff/spc.itp"<br>#include "TRS.itp"<br>#include "EDO.itp"<br>
..<br>[ molecules ]<br>; Compound #mols<br>Protein_chain_A 1<br>Protein_chain_B 1<br>SOL 185<br>SOL 143<br>TRS 1<br>EDO 1<br>SOL 44125<br>
<b><u><br>Conf.gro:</u></b><br>MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE<br> 5354<br> 2GLN N 1 1.458 -1.158 0.739<br> 2GLN H1 2 1.520 -1.083 0.763<br>.......<br> 485HOH HW1 5333 0.221 -3.864 -2.291<br>
485HOH HW2 5334 0.303 -3.946 -2.407<br> 1TRS O1 1 -3.812 -0.471 -2.002<br> 1TRS H13 2 -3.865 -0.443 -1.922<br> 1TRS C1 3 -3.672 -0.469 -1.971<br> 1TRS C 4 -3.635 -0.571 -1.863<br>
1TRS C3 5 -3.711 -0.547 -1.731<br> 1TRS O3 6 -3.694 -0.414 -1.679<br> 1TRS H33 7 -3.746 -0.404 -1.594<br> 1TRS N 8 -3.673 -0.705 -1.911<br> 1TRS H2 9 -3.625 -0.725 -1.996<br>
1TRS H3 10 -3.771 -0.707 -1.927<br> 1TRS H1 11 -3.649 -0.774 -1.842<br> 1TRS C2 12 -3.483 -0.573 -1.840<br> 1TRS O2 13 -3.428 -0.445 -1.806<br> 1TRS H23 14 -3.470 -0.412 -1.722<br>
1EDO OAB 1 0.307 -2.792 0.149<br> 1EDO HAE 2 0.390 -2.826 0.104<br> 1EDO CAA 3 0.239 -2.901 0.212<br> 1EDO CAC 4 0.111 -2.851 0.281<br> 1EDO OAD 5 0.144 -2.763 0.388<br>
1EDO HAF 6 0.060 -2.731 0.432<br> 8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550 0.00000 0.00000 0.00000<br clear="all"><br>How can I fixed these notes(note 1 and note 2)?<br><br>Thanks in advance<br>
-- <br>Ahmet YILDIRIM<br>