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zyj8119

木虫 (著名写手)

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专业: 理论和计算化学

[交流] 【求助成功】自己建了一个GRO FILE，运行的时候出现这个问题已有1人参与

TITLE
29
1MOL NR5* 1 -1.028 -1.752 -1.513
1MOL CH1 2 -0.235 -2.862 -1.279
1MOL CH1 3 1.033 -2.404 -1.049
1MOL NR5* 4 0.991 -1.025 -1.141
1MOL CH1 5 -0.267 -0.648 -1.419
1MOL CH3 6 -2.476 -1.763 -1.738
1MOL H 7 -0.638 -3.868 -1.287
1MOL H 8 1.949 -2.937 -0.823
1MOL H 9 -0.6 0.385 -1.542
1MOL CH2 10 2.129 -0.097 -0.968
1MOL CH2 11 2.652 0.445 -2.297
1MOL H 12 2.906 -0.658 -0.431
1MOL H 13 1.78 0.712 -0.309
1MOL H 14 1.832 0.975 -2.805
1MOL H 15 2.957 -0.394 -2.944
1MOL H 16 -2.994 -1.925 -0.785
1MOL H 17 -2.72 -2.557 -2.453
1MOL H 18 -2.781 -0.79 -2.133
1MOL CH3 19 3.822 1.404 -2.075
1MOL H 20 3.519 2.256 -1.45
1MOL H 21 4.176 1.805 -3.035
1MOL H 22 4.671 0.904 -1.585
2MOL AL 23 -1.33 2.539 0.413
2MOL CL- 24 -1.947 4.416 1.218
2MOL CL- 25 -0.459 2.767 -1.599
2MOL CL- 26 -2.993 1.14 0.18
2MOL CL- 27 0.191 1.553 1.626
下面是TOP文件
;    File 'sys.top' was generated
;    By user: zhu (503)
;    On host: apollo2
;    At date: Wed Mar 12 15:48:05 2008
;
;    This is your topology file
;    DRG
;
; Include forcefield parameters
#include "ffG53a6.itp"

; Include water topology
#include "spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct    fcx       fcy       fcz
1 1    1000    1000    1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
aok in water

[ molecules ]
; Compound       #mols
molecule             1

为什么输入grompp命令最小化能量以后，出现这个问题？

creating statusfile for 1 node...
' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
Cleaning up temporary file grompps5tTct
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 1293

Fatal error:
No such moleculetype molecule

[ Last edited by zyj8119 on 2010-9-9 at 08:26 ]

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