Just check very end of the top file. Make sure the numbers of sol, ions and TOTAL are consistent.
--- Shanshan Qin <[EMAIL PROTECTED]> wrote: > Hi,everyone,I put forward the question yesterday. > When I run the simulation, the system always echo > "Fatal error: number of coordinates in coordinate > file (conf.gro, 12032) does not match topology > (topol.top, 0)". > Mr Abraham has pointed out maybe there is something > wrong with the topol.top file. > Now I put the topol.top here: > > ; > ; Topology file for Coarse Grained DPPC + Water > ; > #include "CG.itp" > > [ system ] > Coase Grained DPPC in Water > > [ molecules ] > ;molecule name nr. > DPPC 512 > WATER 5888 > ; > ; CG.itp: force field file for > ; Coarse Grained DPPC and Water > ; > > [ defaults ] > 1 1 > > [ atomtypes ] > ; type mass charge ptype c6 > c12 > > ; polar type > P 72.0 0.000 A 0.0 > 0.0 > > ; non polar > Na 72.0 0.000 A 0.0 > 0.0 > > ; apolar > C 72.0 0.000 A 0.0 > 0.0 > > ; charged > Q0 72.0 0.000 A 0.0 > 0.0 > Qa 72.0 0.000 A 0.0 > 0.0 > > [ nonbond_params ] > ; i j fund c6 c12 > P P 1 0.21558E-00 > 0.23238E-02 > Na Na 1 0.18108E-00 > 0.19520E-02 > C C 1 0.14660E-00 > 0.15802E-02 > Q0 Q0 1 0.14660E-00 > 0.15802E-02 > Qa Qa 1 0.14660E-00 > 0.15802E-02 > P Na 1 0.14660E-00 > 0.15802E-02 > P C 1 0.77610E-01 > 0.83658E-03 > P Q0 1 0.21558E-00 > 0.23238E-02 > P Qa 1 0.21558E-00 > 0.23238E-02 > Na C 1 0.11210E-00 > 0.12084E-02 > Na Q0 1 0.14660E-00 > 0.15802E-02 > Na Qa 1 0.14660E-00 > 0.15802E-02 > C Q0 1 0.77610E-01 > 0.83658E-03 > C Qa 1 0.77610E-01 > 0.83658E-03 > Q0 Qa 1 0.14660E-00 > 0.15802E-02 > > > ;; Coarse Grained Water Molecule > > [ moleculetype ] > ; name nrexcl > WATER 2 > > [ atoms ] > ; nr type resnr residu atom cgnr > charge mass > 1 P 1 WATER W 1 > 0 72.000 > > ;; Coarse Grained DPPC Molecule > > [ moleculetype ] > ; name nrexxl > DPPC 1 > > [ atoms ] > ; nr type resnr residu atom cgnr > charge mass > 1 Q0 1 DPPC NC3 1 > 1.0 72.000 > 2 Qa 1 DPPC PO4 2 > -1.0 72.000 > 3 Na 1 DPPC GL1 3 > 0 72.000 > 4 Na 1 DPPC GL2 4 > 0 72.000 > 5 C 1 DPPC C1A 5 > 0 72.000 > 6 C 1 DPPC C2A 6 > 0 72.000 > 7 C 1 DPPC C3A 7 > 0 72.000 > 8 C 1 DPPC C4A 8 > 0 72.000 > 9 C 1 DPPC C1B 9 > 0 72.000 > 10 C 1 DPPC C2B 10 > 0 72.000 > 11 C 1 DPPC C3B 11 > 0 72.000 > 12 C 1 DPPC C4B 12 > 0 72.000 > > [ bonds ] > ; ai aj funct length force.c > 1 2 1 0.470 1250 > 2 3 1 0.470 1250 > 3 4 1 0.470 1250 > 3 5 1 0.470 1250 > 5 6 1 0.470 1250 > 6 7 1 0.470 1250 > 7 8 1 0.470 1250 > 4 9 1 0.470 1250 > 9 10 1 0.470 1250 > 10 11 1 0.470 1250 > 11 12 1 0.470 1250 > > [ angles ] > ; i j k funct angle force.c > 2 3 4 2 120.000 25.0 > 2 3 5 2 180.000 25.0 > 3 5 6 2 180.000 25.0 > 5 6 7 2 180.000 25.0 > 6 7 8 2 180.000 25.0 > 4 9 10 2 180.000 25.0 > 9 10 11 2 180.000 25.0 > 10 11 12 2 180.000 25.0 > Since the conf.gro file is rather large,so I will > not paste it here, and the conf.gro seems to be > right.What bothers me most is why my computer can't > recognizeatom coordinates in the topol.top.Can > anyone helpme out?By the way my linux is Fedora > Core5,and the Gromacsedition is 3.3.1.> _______________________________________________ > gmx-users mailing list gmx-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 ____________________________________________________________________________________ We won't tell. Get more on shows you hate to love (and love to hate): Yahoo! TV's Guilty Pleasures list. http://tv.yahoo.com/collections/265 _______________________________________________ gmx-users mailing list gmx-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
