RE: [gmx-users] x2top error in CNT simulation on Gromacs 3.3.3
Send a copy of your ffgmx.n2t, ffgmxbon.itp, and SWNT_6_6_144.pdb files please, if the following does not work. Also I think that the information updated in ffgmxbon.itp might be found in a different file with the 3.3.3 version (I think from looking at previous e-mails that it is ffencadvbon.itp). If any one could let me know I will make an addendum to my site for this new version. (I am about done using GROMACS due to the fact that I am graduating, so I will not be updating mine) ~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA >-Original Message- >From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] >On Behalf Of Hero >Sent: Wednesday, April 23, 2008 5:44 PM >To: gmx-users@gromacs.org >Subject: [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 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 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
Re: [gmx-users] x2top error in CNT simulation
Hero wrote: 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? 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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