[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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