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