[gmx-users] lipid itp file problem

serdar durdagi durdagis at yahoo.de
Sun Jul 6 19:24:17 CEST 2008


Dear all,

I am trying to simulate drug at the binding site of the receptor surrounded by DPPC bilayer system. I have problem at the energy minimisation step. Always, I am getting below error message:

Back Off! I just backed up last.edr to ./#last.edr.8#
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+02
   Number of steps    =          500
Warning: 1-4 interaction between 3642 and 3647 at distance 1.325 which is larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
Step=    0, Dmax= 1.0e-02 nm, Epot=  7.16584e+15 Fmax= 5.29841e+18, atom= 2662
Step=    1, Dmax= 1.0e-02 nm, Epot=  1.19114e+12 Fmax= 2.10320e+14, atom= 3605
Step=    2, Dmax= 1.2e-02 nm, Epot=  1.39843e+10 Fmax= 8.84756e+11, atom= 2662
Step=    3, Dmax= 1.4e-02 nm, Epot=  1.36040e+09 Fmax= 5.31692e+10, atom= 2661
Step=    4, Dmax= 1.7e-02 nm, Epot=  5.09105e+08 Fmax= 2.70368e+09, atom= 3603
Step=    5, Dmax= 2.1e-02 nm, Epot=  3.53172e+08 Fmax= 4.50870e+08, atom= 2661
....

When I try to increase table-extension to more than 1.0, 1-4 interaction always increases.

I checked the  *.gro file, it seems during the minimisation, bonds at protein and drg molecules are fine however, bonds at the DPPC molecules are broken.

I guess problem is at the *.itp file of dppc. I produced *.itp file of DPPC from PRODRG. *itp file of lipid and *.mdp file for energy minimisation are attached below.

Could any body give a clue for the solution? Many thanks in advanced.


Serdar Durdagi

LIPID ITP FILE:

[ moleculetype ]
; Name nrexcl   
MOL      3      

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  MOL      C8     1   -0.033  15.0350
     2       CH2     1  MOL      C1     1    0.008  14.0270
     3       CH2     1  MOL     C45     1    0.008  14.0270
     4       CH2     1  MOL     C44     1    0.009  14.0270
     5       CH2     1  MOL     C43     1    0.008  14.0270
     6       CH2     1  MOL     C42     2    0.000  14.0270
     7       CH2     1  MOL     C41     2    0.000  14.0270
     8       CH2     1  MOL     C40     3    0.000  14.0270
     9       CH2     1  MOL     C39     3    0.000  14.0270
    10       CH2     1  MOL     C38     4    0.000  14.0270
    11       CH2     1  MOL     C37     4    0.000  14.0270
    12       CH2     1  MOL     C36     5    0.000  14.0270
    13       CH2     1  MOL     C35     5    0.000  14.0270
    14       CH2     1  MOL     C34     6    0.000  14.0270
    15       CH2     1  MOL     C33     7    0.036  14.0270
    16         C     1  MOL     C32     7    0.438  12.0110
    17         O     1  MOL     O46     7   -0.551  15.9994
    18        OS     1  MOL     O31     7   -0.160  15.9994
    19       CS1     1  MOL     C13     7    0.237  13.0190
    20       CH2     1  MOL     C12     8    0.000  14.0270
    21        OS     1  MOL     O11     9   -0.256  15.9994
    22         P     1  MOL      P8     9    0.998  30.9738
    23        OM     1  MOL     O10     9   -0.743  15.9994
    24        OM     1  MOL      O9     9   -0.743  15.9994
    25        OS     1  MOL      O4     9   -0.256  15.9994
    26       CH2     1  MOL      C3    10    0.041  14.0270
    27       CH2     1  MOL      C2    10    0.041  14.0270
    28        NL     1  MOL      N1    10    0.918  14.0067
    29       CH3     1  MOL      C6    11    0.000  15.0350
    30       CH3     1  MOL      C5    11    0.000  15.0350
    31       CH3     1  MOL      C7    12    0.000  15.0350
    32       CS2     1  MOL     C14    13    0.242  14.0270
    33        OS     1  MOL     O15    13   -0.162  15.9994
    34         C     1  MOL     C16    13    0.437  12.0110
    35         O     1  MOL     O30    13   -0.553  15.9994
    36       CH2     1  MOL     C17    13    0.036  14.0270
    37       CH2     1  MOL     C18    14    0.000  14.0270
    38       CH2     1  MOL     C19    14    0.000  14.0270
    39       CH2     1  MOL     C20    15    0.000  14.0270
    40       CH2     1  MOL     C21    15    0.000  14.0270
    41       CH2     1  MOL     C22    16    0.000  14.0270
    42       CH2     1  MOL     C23    16    0.000  14.0270
    43       CH2     1  MOL     C24    17    0.000  14.0270
    44       CH2     1  MOL     C25    17    0.000  14.0270
    45       CH2     1  MOL     C26    18    0.000  14.0270
    46       CH2     1  MOL     C27    19    0.008  14.0270
    47       CH2     1  MOL     C28    19    0.008  14.0270
    48       CH2     1  MOL     C29    19    0.008  14.0270
    49       CH2     1  MOL      C9    19    0.009  14.0270
    50       CH3     1  MOL     C10    19   -0.033  15.0350

[ bonds ]
; ai  aj  fu    c0, c1, ...
   1   2   1    0.153    334720.0    0.153    334720.0 ;    C8   C1
   2   3   1    0.153    334720.0    0.153    334720.0 ;    C1  C45
   3   4   1    0.153    334720.0    0.153    334720.0 ;   C45  C44
   4   5   1    0.153    334720.0    0.153    334720.0 ;   C44  C43
   5   6   1    0.153    334720.0    0.153    334720.0 ;   C43  C42
   6   7   1    0.153    334720.0    0.153    334720.0 ;   C42  C41
   7   8   1    0.153    334720.0    0.153    334720.0 ;   C41  C40
   8   9   1    0.153    334720.0    0.153    334720.0 ;   C40  C39
   9  10   1    0.153    334720.0    0.153    334720.0 ;   C39  C38
  10  11   1    0.153    334720.0    0.153    334720.0 ;   C38  C37
  11  12   1    0.153    334720.0    0.153    334720.0 ;   C37  C36
  12  13   1    0.153    334720.0    0.153    334720.0 ;   C36  C35
  13  14   1    0.153    334720.0    0.153    334720.0 ;   C35  C34
  14  15   1    0.153    334720.0    0.153    334720.0 ;   C34  C33
  15  16   1    0.153    334720.0    0.153    334720.0 ;   C33  C32
  16  17   1    0.123    502080.0    0.123    502080.0 ;   C32  O46
  16  18   1    0.136    376560.0    0.136    376560.0 ;   C32  O31
  18  19   1    0.144    251040.0    0.144    251040.0 ;   O31  C13
  19  20   1    0.153    251040.0    0.153    251040.0 ;   C13  C12
  19  32   1    0.152    251040.0    0.152    251040.0 ;   C13  C14
  20  21   1    0.143    251040.0    0.143    251040.0 ;   C12  O11
  21  22   1    0.161    251040.0    0.161    251040.0 ;   O11   P8
  22  23   1    0.148    376560.0    0.148    376560.0 ;    P8  O10
  22  24   1    0.148    376560.0    0.148    376560.0 ;    P8   O9
  22  25   1    0.161    251040.0    0.161    251040.0 ;    P8   O4
  25  26   1    0.143    251040.0    0.143    251040.0 ;    O4   C3
  26  27   1    0.153    334720.0    0.153    334720.0 ;    C3   C2
  27  28   1    0.147    376560.0    0.147    376560.0 ;    C2   N1
  28  29   1    0.147    376560.0    0.147    376560.0 ;    N1   C6
  28  30   1    0.147    376560.0    0.147    376560.0 ;    N1   C5
  28  31   1    0.147    376560.0    0.147    376560.0 ;    N1   C7
  32  33   1    0.144    251040.0    0.144    251040.0 ;   C14  O15
  33  34   1    0.136    376560.0    0.136    376560.0 ;   O15  C16
  34  35   1    0.123    502080.0    0.123    502080.0 ;   C16  O30
  34  36   1    0.153    334720.0    0.153    334720.0 ;   C16  C17
  36  37   1    0.153    334720.0    0.153    334720.0 ;   C17  C18
  37  38   1    0.153    334720.0    0.153    334720.0 ;   C18  C19
  38  39   1    0.153    334720.0    0.153    334720.0 ;   C19  C20
  39  40   1    0.153    334720.0    0.153    334720.0 ;   C20  C21
  40  41   1    0.153    334720.0    0.153    334720.0 ;   C21  C22
  41  42   1    0.153    334720.0    0.153    334720.0 ;   C22  C23
  42  43   1    0.153    334720.0    0.153    334720.0 ;   C23  C24
  43  44   1    0.153    334720.0    0.153    334720.0 ;   C24  C25
  44  45   1    0.153    334720.0    0.153    334720.0 ;   C25  C26
  45  46   1    0.153    334720.0    0.153    334720.0 ;   C26  C27
  46  47   1    0.153    334720.0    0.153    334720.0 ;   C27  C28
  47  48   1    0.153    334720.0    0.153    334720.0 ;   C28  C29
  48  49   1    0.153    334720.0    0.153    334720.0 ;   C29   C9
  49  50   1    0.153    334720.0    0.153    334720.0 ;    C9  C10
  
[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   4   1                                           ;    C8  C44
   2   5   1                                           ;    C1  C43
   3   6   1                                           ;   C45  C42
   4   7   1                                           ;   C44  C41
   5   8   1                                           ;   C43  C40
   6   9   1                                           ;   C42  C39
   7  10   1                                           ;   C41  C38
   8  11   1                                           ;   C40  C37
   9  12   1                                           ;   C39  C36
  10  13   1                                           ;   C38  C35
  11  14   1                                           ;   C37  C34
  12  15   1                                           ;   C36  C33
  13  16   1                                           ;   C35  C32
  14  17   1                                           ;   C34  O46
  14  18   1                                           ;   C34  O31
  15  19   1                                           ;   C33  C13
  16  20   1                                           ;   C32  C12
  16  32   1                                           ;   C32  C14
  17  19   1                                           ;   O46  C13
  18  21   1                                           ;   O31  O11
  18  33   1                                           ;   O31  O15
  19  22   1                                           ;   C13   P8
  19  34   1                                           ;   C13  C16
  20  23   1                                           ;   C12  O10
  20  24   1                                           ;   C12   O9
  20  25   1                                           ;   C12   O4
  20  33   1                                           ;   C12  O15
  21  26   1                                           ;   O11   C3
  21  32   1                                           ;   O11  C14
  22  27   1                                           ;    P8   C2
  23  26   1                                           ;   O10   C3
  24  26   1                                           ;    O9   C3
  25  28   1                                           ;    O4   N1
  26  29   1                                           ;    C3   C6
  26  30   1                                           ;    C3   C5
  26  31   1                                           ;    C3   C7
  32  35   1                                           ;   C14  O30
  32  36   1                                           ;   C14  C17
  33  37   1                                           ;   O15  C18
  34  38   1                                           ;   C16  C19
  35  37   1                                           ;   O30  C18
  36  39   1                                           ;   C17  C20
  37  40   1                                           ;   C18  C21
  38  41   1                                           ;   C19  C22
  39  42   1                                           ;   C20  C23
  40  43   1                                           ;   C21  C24
  41  44   1                                           ;   C22  C25
  42  45   1                                           ;   C23  C26
  43  46   1                                           ;   C24  C27
  44  47   1                                           ;   C25  C28
  45  48   1                                           ;   C26  C29
  46  49   1                                           ;   C27   C9
  47  50   1                                           ;   C28  C10
  
[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   1    111.0       460.2    111.0       460.2 ;    C8   C1  C45
   2   3   4   1    111.0       460.2    111.0       460.2 ;    C1  C45  C44
   3   4   5   1    111.0       460.2    111.0       460.2 ;   C45  C44  C43
   4   5   6   1    111.0       460.2    111.0       460.2 ;   C44  C43  C42
   5   6   7   1    111.0       460.2    111.0       460.2 ;   C43  C42  C41
   6   7   8   1    111.0       460.2    111.0       460.2 ;   C42  C41  C40
   7   8   9   1    111.0       460.2    111.0       460.2 ;   C41  C40  C39
   8   9  10   1    111.0       460.2    111.0       460.2 ;   C40  C39  C38
   9  10  11   1    111.0       460.2    111.0       460.2 ;   C39  C38  C37
  10  11  12   1    111.0       460.2    111.0       460.2 ;   C38  C37  C36
  11  12  13   1    111.0       460.2    111.0       460.2 ;   C37  C36  C35
  12  13  14   1    111.0       460.2    111.0       460.2 ;   C36  C35  C34
  13  14  15   1    111.0       460.2    111.0       460.2 ;   C35  C34  C33
  14  15  16   1    111.0       460.2    111.0       460.2 ;   C34  C33  C32
  15  16  17   1    121.0       502.1    121.0       502.1 ;   C33  C32  O46
  15  16  18   1    120.0       418.4    120.0       418.4 ;   C33  C32  O31
  17  16  18   1    120.0       418.4    120.0       418.4 ;   O46  C32  O31
  16  18  19   1    109.5       334.7    109.5       334.7 ;   C32  O31  C13
  18  19  20   1    109.5       284.5    109.5       284.5 ;   O31  C13  C12
  18  19  32   1    109.5       284.5    109.5       284.5 ;   O31  C13  C14
  20  19  32   1    109.5       251.0    109.5       251.0 ;   C12  C13  C14
  19  20  21   1    111.0       460.2    111.0       460.2 ;   C13  C12  O11
  20  21  22   1    120.0       397.5    120.0       397.5 ;   C12  O11   P8
  21  22  23   1    109.6       397.5    109.6       397.5 ;   O11   P8  O10
  21  22  24   1    109.6       397.5    109.6       397.5 ;   O11   P8   O9
  21  22  25   1    103.0       397.5    103.0       397.5 ;   O11   P8   O4
  23  22  24   1    120.0       585.8    120.0       585.8 ;   O10   P8   O9
  23  22  25   1    109.6       397.5    109.6       397.5 ;   O10   P8   O4
  24  22  25   1    109.6       397.5    109.6       397.5 ;    O9   P8   O4
  22  25  26   1    120.0       397.5    120.0       397.5 ;    P8   O4   C3
  25  26  27   1    109.5       460.2    109.5       460.2 ;    O4   C3   C2
  26  27  28   1    109.5       460.2    109.5       460.2 ;    C3   C2   N1
  27  28  29   1    109.5       376.6    109.5       376.6 ;    C2   N1   C6
  27  28  30   1    109.5       376.6    109.5       376.6 ;    C2   N1   C5
  27  28  31   1    109.5       376.6    109.5       376.6 ;    C2   N1   C7
  29  28  30   1    109.5       376.6    109.5       376.6 ;    C6   N1   C5
  29  28  31   1    109.5       376.6    109.5       376.6 ;    C6   N1   C7
  30  28  31   1    109.5       376.6    109.5       376.6 ;    C5   N1   C7
  19  32  33   1    109.5       284.5    109.5       284.5 ;   C13  C14  O15
  32  33  34   1    109.5       334.7    109.5       334.7 ;   C14  O15  C16
  33  34  35   1    120.0       418.4    120.0       418.4 ;   O15  C16  O30
  33  34  36   1    120.0       418.4    120.0       418.4 ;   O15  C16  C17
  35  34  36   1    121.0       502.1    121.0       502.1 ;   O30  C16  C17
  34  36  37   1    111.0       460.2    111.0       460.2 ;   C16  C17  C18
  36  37  38   1    111.0       460.2    111.0       460.2 ;   C17  C18  C19
  37  38  39   1    111.0       460.2    111.0       460.2 ;   C18  C19  C20
  38  39  40   1    111.0       460.2    111.0       460.2 ;   C19  C20  C21
  39  40  41   1    111.0       460.2    111.0       460.2 ;   C20  C21  C22
  40  41  42   1    111.0       460.2    111.0       460.2 ;   C21  C22  C23
  41  42  43   1    111.0       460.2    111.0       460.2 ;   C22  C23  C24
  42  43  44   1    111.0       460.2    111.0       460.2 ;   C23  C24  C25
  43  44  45   1    111.0       460.2    111.0       460.2 ;   C24  C25  C26
  44  45  46   1    111.0       460.2    111.0       460.2 ;   C25  C26  C27
  45  46  47   1    111.0       460.2    111.0       460.2 ;   C26  C27  C28
  46  47  48   1    111.0       460.2    111.0       460.2 ;   C27  C28  C29
  47  48  49   1    111.0       460.2    111.0       460.2 ;   C28  C29   C9
  48  49  50   1    111.0       460.2    111.0       460.2 ;   C29   C9  C10
  
[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
  16  15  18  17   2      0.0 1673.6        0.0 1673.6   ; imp   C32  C33  O31  O46
  34  33  36  35   2      0.0 1673.6        0.0 1673.6   ; imp   C16  O15  C17  O30
  19  18  32  20   2     35.3  836.8       35.3  836.8   ; imp   C13  O31  C14  C12
  22  21  24  23   2     35.3  836.8       35.3  836.8   ; imp    P8  O11   O9  O10
  28  27  29  30   2     35.3  836.8       35.3  836.8   ; imp    N1   C2   C6   C5
   4   3   2   1   1      0.0    5.9 3      0.0    5.9 3 ; dih   C44  C45   C1   C8
   5   4   3   2   1      0.0    5.9 3      0.0    5.9 3 ; dih   C43  C44  C45   C1
   6   5   4   3   1      0.0    5.9 3      0.0    5.9 3 ; dih   C42  C43  C44  C45
   7   6   5   4   1      0.0    5.9 3      0.0    5.9 3 ; dih   C41  C42  C43  C44
   8   7   6   5   1      0.0    5.9 3      0.0    5.9 3 ; dih   C40  C41  C42  C43
   9   8   7   6   1      0.0    5.9 3      0.0    5.9 3 ; dih   C39  C40  C41  C42
  10   9   8   7   1      0.0    5.9 3      0.0    5.9 3 ; dih   C38  C39  C40  C41
  11  10   9   8   1      0.0    5.9 3      0.0    5.9 3 ; dih   C37  C38  C39  C40
  12  11  10   9   1      0.0    5.9 3      0.0    5.9 3 ; dih   C36  C37  C38  C39
  13  12  11  10   1      0.0    5.9 3      0.0    5.9 3 ; dih   C35  C36  C37  C38
  14  13  12  11   1      0.0    5.9 3      0.0    5.9 3 ; dih   C34  C35  C36  C37
  15  14  13  12   1      0.0    5.9 3      0.0    5.9 3 ; dih   C33  C34  C35  C36
  16  15  14  13   1      0.0    5.9 3      0.0    5.9 3 ; dih   C32  C33  C34  C35
  14  15  16  18   1      0.0    0.4 6      0.0    0.4 6 ; dih   C34  C33  C32  O31
  15  16  18  19   1    180.0   16.7 2    180.0   16.7 2 ; dih   C33  C32  O31  C13
  32  19  18  16   1      0.0    3.8 3      0.0    3.8 3 ; dih   C14  C13  O31  C32
  18  19  20  21   1      0.0    5.9 3      0.0    5.9 3 ; dih   O31  C13  C12  O11
  33  32  19  18   1      0.0    5.9 3      0.0    5.9 3 ; dih   O15  C14  C13  O31
  22  21  20  19   1      0.0    3.8 3      0.0    3.8 3 ; dih    P8  O11  C12  C13
  20  21  22  25   1      0.0    1.0 3      0.0    1.0 3 ; dih   C12  O11   P8   O4
  20  21  22  25   1      0.0    3.1 2      0.0    3.1 2 ; dih   C12  O11   P8   O4
  26  25  22  21   1      0.0    1.0 3      0.0    1.0 3 ; dih    C3   O4   P8  O11
  26  25  22  21   1      0.0    3.1 2      0.0    3.1 2 ; dih    C3   O4   P8  O11
  22  25  26  27   1      0.0    3.8 3      0.0    3.8 3 ; dih    P8   O4   C3   C2
  28  27  26  25   1      0.0    5.9 3      0.0    5.9 3 ; dih    N1   C2   C3   O4
  26  27  28  31   1      0.0    3.8 3      0.0    3.8 3 ; dih    C3   C2   N1   C7
  19  32  33  34   1      0.0    3.8 3      0.0    3.8 3 ; dih   C13  C14  O15  C16
  32  33  34  36   1    180.0   16.7 2    180.0   16.7 2 ; dih   C14  O15  C16  C17
  37  36  34  33   1      0.0    0.4 6      0.0    0.4 6 ; dih   C18  C17  C16  O15
  38  37  36  34   1      0.0    5.9 3      0.0    5.9 3 ; dih   C19  C18  C17  C16
  39  38  37  36   1      0.0    5.9 3      0.0    5.9 3 ; dih   C20  C19  C18  C17
  40  39  38  37   1      0.0    5.9 3      0.0    5.9 3 ; dih   C21  C20  C19  C18
  41  40  39  38   1      0.0    5.9 3      0.0    5.9 3 ; dih   C22  C21  C20  C19
  42  41  40  39   1      0.0    5.9 3      0.0    5.9 3 ; dih   C23  C22  C21  C20
  43  42  41  40   1      0.0    5.9 3      0.0    5.9 3 ; dih   C24  C23  C22  C21
  44  43  42  41   1      0.0    5.9 3      0.0    5.9 3 ; dih   C25  C24  C23  C22
  45  44  43  42   1      0.0    5.9 3      0.0    5.9 3 ; dih   C26  C25  C24  C23
  46  45  44  43   1      0.0    5.9 3      0.0    5.9 3 ; dih   C27  C26  C25  C24
  47  46  45  44   1      0.0    5.9 3      0.0    5.9 3 ; dih   C28  C27  C26  C25
  48  47  46  45   1      0.0    5.9 3      0.0    5.9 3 ; dih   C29  C28  C27  C26
  49  48  47  46   1      0.0    5.9 3      0.0    5.9 3 ; dih    C9  C29  C28  C27
  50  49  48  47   1      0.0    5.9 3      0.0    5.9 3 ; dih   C10   C9  C29  C28

MDP FILE:

title                   = vals
cpp                     = /usr/bin/cpp
define                  = -DFLEXIBLE
constraints             = none
integrator              = steep
dt                      = 0.002         ; ps !
nsteps                  = 500
nstlists                = 10
ns_type                 = grid
rlist                   = 1.0
coulombtype             = PME
rcoulomb                = 1.0
vdwtype                 = cut-off
rvdw                    = 1.0
fourierspacing          = 0.12
fourier_nx              = 0
fourier_ny              = 0
fourier_nz              = 0
pme_order               = 4
ewald_rtol              = 1e-5
optimize_fft            = yes
;
;       Energy minimizing stuff
;
emtol                   = 100.0
emsteps                 = 0.01






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