Dear Tsjerk, I will ask you one thing but please do not get angry (I know you are not a private tutor but I need your helps).
How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can you suggest a tutorial?) Thanks 2011/3/31 Mark Abraham <[email protected]> > On 31/03/2011 5:18 PM, ahmet yıldırım wrote: > > 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 > > > This is an integer. See > http://en.wikipedia.org/wiki/Scientific_notation#E_notation and > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > > *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. > > > See Tsjerk's email. > > Mark > > > * > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
