[gmx-users] coarse grain topology file

Shanshan Qin sansanqin00 at mails.tsinghua.edu.cn
Sat Mar 24 14:28:02 CET 2007


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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