Re: [gmx-users] Can you help me ?
Try put Cl- under [ molecules ] [EMAIL PROTECTED] wrote: when I use the following command ,there always a error message.Can you help me ? Thank you very much ! command: grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr error message: . . creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 3 bonded neighbours for IN4 1 Excluding 2 bonded neighbours for SOL 4145 Cleaning up temporary file gromppD2IkOr --- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 1264 Fatal error: No such moleculetype Cl --- enviroment: ++ extra information: OS: Red Hat Linux AS4 fftw: fftw-3.1.2.tar.tar gromacs: gromacs-3.3.tar.gz installation : 1.fftw ./configure --enable-float make make install 2. gromacs ./configure CPPFLAGS=-I/gromacs/gromacs-3.3/include LDFLAGS=-L/gromacs/fftw-3.1.2/libbench2 make make install ++ *用搜狗拼音写邮件，体验更流畅的中文输入 http://goto.mail.sohu.com/goto.php3?code=mailadt-ta ___ 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
RE: [gmx-users] Can you help me ?
It seems the ions type not set. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, April 06, 2007 10:15 AM To: gmx-users@gromacs.org Subject: [gmx-users] Can you help me ? when I use the following command ,there always a error message.Can you help me ? Thank you very much ! command: grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr error message: . . creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 3 bonded neighbours for IN4 1 Excluding 2 bonded neighbours for SOL 4145 Cleaning up temporary file gromppD2IkOr --- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 1264 Fatal error: No such moleculetype Cl --- enviroment: ++ extra information: OS: Red Hat Linux AS4 fftw: fftw-3.1.2.tar.tar gromacs: gromacs-3.3.tar.gz installation : 1.fftw ./configure --enable-float make make install 2. gromacs ./configureCPPFLAGS=-I/gromacs/gromacs-3.3/include LDFLAGS=-L/gromacs/fftw-3.1.2/libbench2 make make install ++ *用搜狗拼音写邮件，体验更流畅的中文输入 http://goto.mail.sohu.com/goto.php3?code=mailadt-ta ___ 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] Can you help me ?
[EMAIL PROTECTED] wrote: when I use the following command ,there always a error message.Can you help me ? Thank you very much ! command: grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr error message: . . creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 3 bonded neighbours for IN4 1 Excluding 2 bonded neighbours for SOL 4145 Cleaning up temporary file gromppD2IkOr --- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 1264 Fatal error: No such moleculetype Cl --- Your topology is specifying a molecule type that doesn't appear in your force field. Check that you've included ions.itp and that its contents match your topology as far as atom and molecule names go. Mark ___ 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
