[gmx-users] coarse grain topology file
yuemin liu
liucan1 at yahoo.com
Sat Mar 24 14:53:34 CET 2007
Just check very end of the top file. Make sure the
numbers of sol, ions and TOTAL are consistent.
--- Shanshan Qin <sansanqin00 at mails.tsinghua.edu.cn>
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.>
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