[gmx-users] coarse grain topology file
Yang Ye
leafyoung81-group at yahoo.com
Sat Mar 24 16:12:52 CET 2007
yuemin liu wrote:
> Just check very end of the top file. Make sure the
> numbers of sol, ions and TOTAL are consistent.
>
It is in the [molecules] section.
> --- 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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