[gmx-users] x2top error in CNT simulation on Gromacs 3.3.3
Dear All, I am trying to simulate water flow in CNT and just followed the website: http://cs86.com/CNSE/SWNT.htm I did the following: 1. ffgmx.n2t must change this files name to ffencadv.n2t and add the following 2 lines: C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT double bonded Carbon 2. ffgmxbon.itp add the following line to it: # [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. # [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 # [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 # But when I ran: x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp Error message appeared: Can not find forcefield for atom C-1 with 2 bonds . Can not find forcefield for atom C-143 with 2 bonds Can not find forcefield for atom C-144 with 2 bonds --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 144 atoms --- Could you please tell me what is the problem? This works on Gromacs 3.3.1 Thank you very much! Jue Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] x2top error in CNT simulation
Dear All, I am trying to simulate water flow in CNT and just followed the website: http://cs86.com/CNSE/SWNT.htm I did the following: 1. ffgmx.n2t must change this files name to ffencadv.n2t and add the following 2 lines: C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT double bonded Carbon 2. ffgmxbon.itp add the following line to it: # [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. # [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 # [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 # But when I ran: x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp Error message appeared: Can not find forcefield for atom C-143 with 2 bonds Can not find forcefield for atom C-144 with 2 bonds --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 144 atoms --- Could you please tell me what is the problem? Thank you very much! Jue Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: x2top error in CNT simulation (David van der Spoel)
Dear Gromacs, Actually, the error is for all the 144 atoms on SWNT_6_6_144: when I ran: x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp Error message appeared: Can not find forcefield for atom C-1 with 2 bonds . Can not find forcefield for atom C-143 with 2 bonds Can not find forcefield for atom C-144 with 2 bonds --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 144 atoms --- Could you please tell me what is the problem? Suppose this code should work without any problems since it has been on web for a long while. Or problems showed up after Gromacs 3.3? Thanks a lot! Jue Dear All, I am trying to simulate water flow in CNT and just followed the website: http://cs86.com/CNSE/SWNT.htm I did the following: 1. ffgmx.n2t must change this files name to ffencadv.n2t and add the following 2 lines: C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT double bonded Carbon 2. ffgmxbon.itp add the following line to it: # [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. # [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 # [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 # But when I ran: x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp Error message appeared: Can not find forcefield for atom C-143 with 2 bonds Can not find forcefield for atom C-144 with 2 bonds --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 144 atoms --- Could you please tell me what is the problem? x2top -pbc where are these atoms, on the edge of the CNT? Is your box size correct such that you have a periodic CNT? Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] CNT
Hello, I plan to insert water molecules into a Single Wall NanoTube, I have generated the structure file of SWNT, but when I use: pdb2gmx -f SWNT_6_6_144.pdb -p SWNT.top -o SWNT.gro to form the gro file, I got the following error: Fatal error: Residue 'UNK' not found in residue topology database Could you please help me out? Thank you very much! Jue Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: CNT
Hello, when I follow http://cs86.com/CNSE/SWNT.htm and ran: x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp I got the following message: Can not find forcefield for atom C-143 with 2 bonds Can not find forcefield for atom C-144 with 2 bonds --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 144 atoms --- Could you please tell me what is the problem? Thank you very much! Jue Message: 4 Date: Mon, 21 Apr 2008 13:21:12 -0400 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] CNT To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Quoting Hero [EMAIL PROTECTED]: Hello, I plan to insert water molecules into a Single Wall NanoTube, I have generated the structure file of SWNT, but when I use: pdb2gmx -f SWNT_6_6_144.pdb -p SWNT.top -o SWNT.gro to form the gro file, I got the following error: Fatal error: Residue 'UNK' not found in residue topology database pdb2gmx is not magic; see here: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database There is also a very detailed link about CNT preparation that was provided to you earlier across this list: http://cs86.com/CNSE/SWNT.htm -Justin Could you please help me out? Thank you very much! Jue Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Water in graphite plates
Dear All, I want to model water transport sandwitched within two graphite surfaces. Do you know how to generate the structure file of graphite surface? Thank you very much! Hero Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] water flow in CNT
Dear All, I am simulating water transport in CNT under pressure. If I use periodic boundary conditions, how can I scale the water velocity? Otherwise the velocity will be going to heaven! Thank you very much! Hero Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] water in channel by Dowser
Dear Gramacs, Anybody know where I can get Dowser for water in channel? Thanks a lot! [gmx-users] water in channel Eric Jakobsson jake at ncsa.uiuc.edu Mon Jan 19 22:50:02 CET 2004 Previous message: [gmx-users] water in channel Next message: [gmx-users] water in channel Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Approach # 2) will not work for all channels. We published a paper in Biophys. J. a number of years ago in which we looked at water motion in the gramicidin channel with the protein immobile but the water at 300 K. The water moved locally in the normal way, but had no motion along the channel at all. I am sure if we had started with the channel empty and the gramicidin frozen, it would never have filled, at least not in any reasonable time. On the other hand, for some channels if you don't immobilize them and you don't have contents in the lumen, the lumenal structure will become unstable. So approach # 1) (Dowser or some equivalent method) is the better way, based on our group's experience. Eric At 11:31 AM 1/19/2004 -0500, you wrote: I can think of 2 options: 1) There is a program called Dowser put out by J. Hermans' lab at UNC-Chapel hill. It usually works very well. 2) You can position restrain the channel and allow water and bilayer to move freely during MD. It should not take long for water to enter the channel ... that is, providing that it is actually supposed to do so. Water is probably the fastest diffusing species in your system. You can take advantage of this. David -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= David Bostick Office: 262 Venable Hall Dept. of Physics and Astronomy Phone: (919)962-0165 Program in Molecular and Cellular Biophysics UNC-Chapel Hill CB #3255 Phillips Hall dbostick at physics.unc.edu Chapel Hill, NC 27599 http://www.unc.edu/~dbostick =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- On Mon, 19 Jan 2004, Itamar Kass wrote: Hi all, I am currently working on a channel in a DMPC bilayer (and water). After inserting the channel into the bilayer (using Graham's modified mdrun) I am facing a new problem. I want to put water in the channel and did not succeed in doing it. Using pr simulation I did not succeed, then I tried to use genbox, but it puts water in the membrane also. Does someone have an idea or face it and has a solution? Thank you, Itamar. Computers are like airconditioners... They don't work well with Windows open. === | Itamar Kass | The Alexander Silberman | Institute of Life Sciences | Department of Biological Chemistry | The Hebrew University, Givat-Ram | Jerusalem, 91904, Israel | Tel: +972-(0)2-6585146 | Fax: +972-(0)2-6584329 | Email: ikass at cc.huji.ac.il | Homepage: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html ___ gmx-users mailing list gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 4021 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 fax 217-244-2909 (Currently on leave to the National Institutes of Health in Bethesda, Maryland, to be Director of the NIGMS Center for Bioinformatics and Computational Biology and Chair of the NIH Biomedical Information Science and Technology Initiative Consortium, but maintaining my research lab at Illinois by periodic commuting. My usual schedule is four days a week at NIH and three days a week at Illinois.) Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] structure files of water and CNT
Hello, I am a new user of Gromacs and want to simulate water transport through Carbon nanotubes. Where can I find structure files of water and CNT? Thank you so much! Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Water flow through Carbon Nanotube
Hello, I am a new user of Gromacs and trying to simulate water flowing in nanotubes. Can I get some idea on how to do this? Where can I have a sample? Thank you very much! Jue Chen Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] How can I install Gromacs on Window XP?
Hello, How can I install Gromacs on Window XP? Thanks a lot! Hero __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
