Re: [gmx-users] protein-DNA simulation with Amber port
You need to put the atom types defined in ffamber under [ atoms ] as replacement of original 1 amber99_54 1 SOL OW 1 -0.82 15.99940 2 amber99_55 1 SOLHW1 1 0.41 1.00800 3 amber99_55 1 SOLHW2 1 0.41 1.00800 It is good to embrace it with some C preprocessor so as to make SPC still works for other force field, #ifdef (_FF_AMBER99) 1 amber99_54 1 SOL OW 1 -0.82 15.99940 2 amber99_55 1 SOLHW1 1 0.41 1.00800 3 amber99_55 1 SOLHW2 1 0.41 1.00800 #else 1 OW 1SOL OW 1 -0.82 2 HW 1SOLHW1 1 0.41 3 HW 1SOLHW2 1 0.41 #endif TJ Piggot wrote: Hi, If i remember correctly i also got this error with spc (and spc/e) and the ffamber port. However i was only playing around in testing different water models and did not spend ages trying to fix this problem because i use tip3p or tip4p for most of my runs. So as to the error i am not sure, however if you try one of the tip*p water models i think that you should not get this error (remember to have #include ffamber_tip*p in your .top file). Sorry i can't be of more help Tom --On Friday, June 01, 2007 01:25:22 -0700 Alaguraj Veluchamy [EMAIL PROTECTED] wrote: Dear Gmx-users, I have followed http://folding.stanford.edu/ffamber/ for porting amber in Gromacs and i am trying to simulate protein-DNA complex. Preprocessing the topology files gives error as below: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22# checking input for internal consistency... calling /lib/cpp -traditional... processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations Cleaning up temporary file gromppkzsTQq Fatal error: [ file /usr/local/gromacs/share/top/spc.itp, line 41 ]: Atom index (1) in settles out of bounds (1-0) I checked at the spc.itp file and found that the line 41 is: [ settles ] ; OWfunct doh dhh 1 1 0.1 0.16333 and i am using em.mdp file: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I tried the earlier post suggestion: that include spc.itp line must be before the [molecule] section, but still gives the same error as: Fatal error: [ file /usr/local/gromacs/share/top/spc.itp, line 41 ]: Atom index (1) in settles out of bounds (1-0) Thanks and regards -Alaguraj.V ALAGURAJ VELUCHAMY c/o Dr.S.KRISHNASWAMY, CENTRE OF EXCELLENCE IN BIOINFORMATICS, MADURAI KAMARAJ UNIVERSITY, MADURAI, TN. Ph:09486148690 __ Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out. -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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 begin:vcard fn:Yang Ye n:Yang;Ye email;internet:[EMAIL PROTECTED] x-mozilla-html:TRUE version:2.1 end:vcard ___ 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] protein-DNA simulation with Amber port
Dear Gmx-users, I have followed http://folding.stanford.edu/ffamber/ for porting amber in Gromacs and i am trying to simulate protein-DNA complex. Preprocessing the topology files gives error as below: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22# checking input for internal consistency... calling /lib/cpp -traditional... processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations Cleaning up temporary file gromppkzsTQq Fatal error: [ file /usr/local/gromacs/share/top/spc.itp, line 41 ]: Atom index (1) in settles out of bounds (1-0) I checked at the spc.itp file and found that the line 41 is: [ settles ] ; OWfunct doh dhh 1 1 0.1 0.16333 and i am using em.mdp file: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I tried the earlier post suggestion: that include spc.itp line must be before the [molecule] section, but still gives the same error as: Fatal error: [ file /usr/local/gromacs/share/top/spc.itp, line 41 ]: Atom index (1) in settles out of bounds (1-0) Thanks and regards -Alaguraj.V ALAGURAJ VELUCHAMY c/o Dr.S.KRISHNASWAMY, CENTRE OF EXCELLENCE IN BIOINFORMATICS, MADURAI KAMARAJ UNIVERSITY, MADURAI, TN. Ph:09486148690 - Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out.___ 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] protein-DNA simulation with Amber port
spc/e works fine for me with ffAMBER03. Are you sure the ordering of your top-file is correct? Check that the [ molecules ] section in correctly ordered. 1 jun 2007 kl. 14.55 skrev TJ Piggot: Hi, If i remember correctly i also got this error with spc (and spc/e) and the ffamber port. However i was only playing around in testing different water models and did not spend ages trying to fix this problem because i use tip3p or tip4p for most of my runs. So as to the error i am not sure, however if you try one of the tip*p water models i think that you should not get this error (remember to have #include ffamber_tip*p in your .top file). Sorry i can't be of more help Tom --On Friday, June 01, 2007 01:25:22 -0700 Alaguraj Veluchamy [EMAIL PROTECTED] wrote: Dear Gmx-users, I have followed http://folding.stanford.edu/ffamber/ for porting amber in Gromacs and i am trying to simulate protein-DNA complex. Preprocessing the topology files gives error as below: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22# checking input for internal consistency... calling /lib/cpp -traditional... processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations Cleaning up temporary file gromppkzsTQq Fatal error: [ file /usr/local/gromacs/share/top/spc.itp, line 41 ]: Atom index (1) in settles out of bounds (1-0) I checked at the spc.itp file and found that the line 41 is: [ settles ] ; OWfunct doh dhh 1 1 0.1 0.16333 and i am using em.mdp file: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I tried the earlier post suggestion: that include spc.itp line must be before the [molecule] section, but still gives the same error as: Fatal error: [ file /usr/local/gromacs/share/top/spc.itp, line 41 ]: Atom index (1) in settles out of bounds (1-0) Thanks and regards -Alaguraj.V ALAGURAJ VELUCHAMY c/o Dr.S.KRISHNASWAMY, CENTRE OF EXCELLENCE IN BIOINFORMATICS, MADURAI KAMARAJ UNIVERSITY, MADURAI, TN. Ph:09486148690 __ Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out. -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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 ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ 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] protein-DNA simulation with Amber port
Figured it out was just being a bit slow. I hadn't include an #ifdef _FF_AMBER statement in spce.itp or spc.itp Thanks Erik and Mark Tom --On Friday, June 01, 2007 23:35:22 +1000 Mark Abraham [EMAIL PROTECTED] wrote: TJ Piggot wrote: Hi I have just checked again by trying to set up a run again using spc/e with amber03. I still get this same error. I am sure the order in the [ molecules ] section is correct, and it is the same order as in the .top file with tip3p or tip4p which both work fine. The only difference between the setup's is the -water option given to pdb2gmx and the -cs option in genbox How do the contents of the water .itp files differ? 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 -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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
