Hi Ahmet, As suggested, it's better to break up your molecule into smaller charge groups. Note that charge groups don't need to have zero charge, nor integer charge. In your case, I'd suggest two COH groups for EDO, which will have zero net charge each, and for TRS I'd take the COH groups as separate charge groups. I also note that the COH groups, although chemically identical - H3NC(COH)3, right?-, have different charges. That doesn't seem proper.
Hope it helps, Tsjerk 2011/3/31 ahmet yıldırım <ahmedo...@gmail.com>: > 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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands
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