Re: [gmx-users] the total charge of system is not an integer
On 5/04/2011 3:57 PM, ahmet yıldırım wrote: Dear Tsjerk, 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 nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 1 *0.000* 14.0270 4 CH2 1 EDO CAC 1 *0.000* 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 can you show me on the itp file? how do I seperate two COH groups? Please help me We didn't say to use zero *charges*. We said you need small charge groups. Since EDO is neutral, then by symmetry each half must also be neutral. Have a look at the way charge groups are used in the .rtp file for your forcefield. You need to do similar things. If you don't understand the file formats yet, you need to read up on chapter 5 of the manual. Mark -- gmx-users mailing listgmx-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
Re: [gmx-users] the total charge of system is not an integer
Dear Mark, Now, are the files correct? *EDO.itp*: [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC *2*0.080 14.0270 5OA 1 EDO OAD *2* -0.111 15.9994 6 H 1 EDO HAF *2 * 0.031 1.0080 *TRS.itp:* [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRSC *3*0.055 12.0110 5 CH2 1 TRS C3* 4 * 0.049 14.0270 6OA 1 TRS O3 *4* -0.205 15.9994 7 H 1 TRS H33* 4*0.019 1.0080 8NL 1 TRS N* 5*0.206 14.0067 9 H 1 TRS H2 * 5*0.004 1.0080 10 H 1 TRSH3 *5*0.004 1.0080 11 H 1 TRSH1 *5 * 0.004 1.0080 12 CH2 1 TRS C2 *6 * 0.150 14.0270 13OA 1 TRS O2 *6* -0.205 15.9994 14 H 1 TRS H23* 6*0.019 1.0080 Thanks for your helps 05 Nisan 2011 09:03 tarihinde Mark Abraham mark.abra...@anu.edu.au yazdı: On 5/04/2011 3:57 PM, ahmet yıldırım wrote: Dear Tsjerk, 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 nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 1*0.000* 14.0270 4 CH2 1 EDO CAC 1*0.000* 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 can you show me on the itp file? how do I seperate two COH groups? Please help me We didn't say to use zero *charges*. We said you need small charge groups. Since EDO is neutral, then by symmetry each half must also be neutral. Have a look at the way charge groups are used in the .rtp file for your forcefield. You need to do similar things. If you don't understand the file formats yet, you need to read up on chapter 5 of the manual. Mark -- gmx-users mailing listgmx-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 -- Ahmet YILDIRIM -- gmx-users mailing listgmx-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
Re: [gmx-users] the total charge of system is not an integer
On 5/04/2011 9:59 PM, ahmet yıldırım wrote: Dear Mark, Now, are the files correct? They're well-formed, but you've not taken Tsjerk's advice and arranged for (COH)3(NH3+)C to have charges consistent with its symmetry. When people donate their time to you, please use it or demonstrate why you shouldn't :-) Mark *EDO.itp*: [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC *2*0.080 14.0270 5OA 1 EDO OAD *2* -0.111 15.9994 6 H 1 EDO HAF *2 * 0.031 1.0080 *TRS.itp:* [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRSC *3*0.055 12.0110 5 CH2 1 TRS C3 *4 * 0.049 14.0270 6OA 1 TRS O3 *4* -0.205 15.9994 7 H 1 TRS H33 *4*0.019 1.0080 8NL 1 TRS N *5*0.206 14.0067 9 H 1 TRS H2 *5*0.004 1.0080 10 H 1 TRSH3 *5*0.004 1.0080 11 H 1 TRSH1 *5 * 0.004 1.0080 12 CH2 1 TRS C2 *6 * 0.150 14.0270 13OA 1 TRS O2 *6* -0.205 15.9994 14 H 1 TRS H23 *6*0.019 1.0080 Thanks for your helps 05 Nisan 2011 09:03 tarihinde Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au yazdı: On 5/04/2011 3:57 PM, ahmet yıldırım wrote: Dear Tsjerk, 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 nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 1 *0.000* 14.0270 4 CH2 1 EDO CAC 1 *0.000* 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 can you show me on the itp file? how do I seperate two COH groups? Please help me We didn't say to use zero *charges*. We said you need small charge groups. Since EDO is neutral, then by symmetry each half must also be neutral. Have a look at the way charge groups are used in the .rtp file for your forcefield. You need to do similar things. If you don't understand the file formats yet, you need to read up on chapter 5 of the manual. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-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
Re: [gmx-users] the total charge of system is not an integer
Dear Tsjerk, 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 nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 1*0.000* 14.0270 4 CH2 1 EDO CAC 1*0.000* 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 can you show me on the itp file? how do I seperate two COH groups? Please help me 31 Mart 2011 12:10 tarihinde Tsjerk Wassenaar tsje...@gmail.com yazdı: Hi Ahmet, Why would I get angry? :) Sending a reply to the list will not usually be taken as asking for private tutoring... As Mark pointed out, you need to get familiar with the format of the files. That's the first thing you should do if you get to the point of needing to use non standard topologies. Read the manual, look at existing files. As for the immediate question, under the [ atoms ] section is a line indicating which column denotes what. You'd need to modify the columns 'cgnr' (charge group number) and probably 'charge'. For finding proper charge groups, in general you best draw your molecule, with the charges added, and then see which atoms would almost naturally group together. TRS.itp: .. [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 Hope it helps, Tsjerk 2011/3/31 ahmet yıldırım ahmedo...@gmail.com: 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 mark.abra...@anu.edu.au 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: -1.50e+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 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 7 H 1 TRS H33 20.019 1.0080 8NL 1 TRS N 20.206 14.0067 9 H 1 TRS H2 20.004 1.0080 10 H 1 TRS H3 20.004 1.0080 11 H 1 TRS H1 20.004 1.0080 12 CH2 1 TRS C2 2
Re: [gmx-users] the total charge of system is not an integer
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: -1.50e+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 0.0 0.0 -4.06550 0.0 0.0 0.0 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
Re: [gmx-users] the total charge of system is not an integer
On 31/03/2011 5:18 PM, ahmet y?ld?r?m 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: -1.50e+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 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 7 H 1 TRS H33 20.019 1.0080 8NL 1 TRS N 20.206 14.0067 9 H 1 TRS H2 20.004 1.0080 10 H 1 TRS H3 20.004 1.0080 11 H 1 TRS H1 20.004 1.0080 12 CH2 1 TRS C2 20.050 14.0270 13OA 1 TRS O2 2 -0.205 15.9994 14 H 1 TRS H23 20.019 1.0080 ... _*EDO.itp*_ ... [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 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 TRS1 EDO1 SOL 44125 *_ Conf.gro:_* MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 ... 485HOHHW1 5333 0.221 -3.864 -2.291 485HOHHW2 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 C4 -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 N8 -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 0.0 0.0 -4.06550 0.0 0.0 0.0 How can I fixed these notes(note 1 and note 2)? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-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
Re: [gmx-users] the total charge of system is not an integer
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 mark.abra...@anu.edu.au 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: -1.50e+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 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 7 H 1 TRS H33 20.019 1.0080 8NL 1 TRS N 20.206 14.0067 9 H 1 TRS H2 20.004 1.0080 10 H 1 TRS H3 20.004 1.0080 11 H 1 TRS H1 20.004 1.0080 12 CH2 1 TRS C2 20.050 14.0270 13OA 1 TRS O2 2 -0.205 15.9994 14 H 1 TRS H23 20.019 1.0080 ... *EDO.itp* ... [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 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 TRS1 EDO1 SOL 44125 * Conf.gro:* MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 ... 485HOHHW1 5333 0.221 -3.864 -2.291 485HOHHW2 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 C4 -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 N8 -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 0.0 0.0 -4.06550 0.0 0.0 0.0 How can I fixed these notes(note 1 and note 2)? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-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 -- Ahmet YILDIRIM -- gmx-users mailing listgmx-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
Re: [gmx-users] the total charge of system is not an integer
On 31/03/2011 6:17 PM, ahmet yıldırım wrote: 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?) You'll need to become familiar with the file format, so that you know what all the columns of data mean, so you know where the charge groups are specified. Chapter 5 of the manual is your first port of call. If you have read that and still have questions about detail, please ask on the list :-) Mark 2011/3/31 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au 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: -1.50e+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 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 7 H 1 TRS H33 20.019 1.0080 8NL 1 TRS N 20.206 14.0067 9 H 1 TRS H2 20.004 1.0080 10 H 1 TRS H3 20.004 1.0080 11 H 1 TRS H1 20.004 1.0080 12 CH2 1 TRS C2 20.050 14.0270 13OA 1 TRS O2 2 -0.205 15.9994 14 H 1 TRS H23 20.019 1.0080 ... _*EDO.itp*_ ... [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 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 TRS1 EDO1 SOL 44125 *_ Conf.gro:_* MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 ... 485HOHHW1 5333 0.221 -3.864 -2.291 485HOHHW2 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 C4 -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 N8 -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 0.0 0.0 -4.06550
Re: [gmx-users] the total charge of system is not an integer
Hi Ahmet, Why would I get angry? :) Sending a reply to the list will not usually be taken as asking for private tutoring... As Mark pointed out, you need to get familiar with the format of the files. That's the first thing you should do if you get to the point of needing to use non standard topologies. Read the manual, look at existing files. As for the immediate question, under the [ atoms ] section is a line indicating which column denotes what. You'd need to modify the columns 'cgnr' (charge group number) and probably 'charge'. For finding proper charge groups, in general you best draw your molecule, with the charges added, and then see which atoms would almost naturally group together. TRS.itp: .. [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 Hope it helps, Tsjerk 2011/3/31 ahmet yıldırım ahmedo...@gmail.com: 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 mark.abra...@anu.edu.au 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: -1.50e+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
