[gmx-users] The energy minimization....

Sampo Karkola sampo.karkola at helsinki.fi
Thu Aug 16 10:39:57 CEST 2007


Hi,

I struggled with a similar minimisation problem with NADP (NDPP topology
in ffG43a1). Then I got a suggestion from a colleague in Prof. Ho"ltje's
group in Dusseldorf, that the atom naming should be changed from eg.
AC5* to something with only three characters, eg. C10. I renamed (and
only renamed) all the atoms with a unique running number and got rid of
the problem. I'm not sure if this will help you but it worked for me.

Hope it helps,

Sampo

mjduan at smail.hust.edu.cn wrote:
> http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.html
> 
> 
> 
> Mark:
> I am sorry to disturb you. I'm a beginner of GROMACS and this 
> "mailing-list" system. I even don't know how to replay a post directly. 
> And yesterday I haven't seen your replay because the list title changed, 
> sorry again!
> 
> About the problem, I haven't resolved it yet. The .top file of my ATP 
> molecule is generated by the pdb2gmx, and the coordinates of each atom 
> adopted to the pdb file. The force file is ffG43a2. Whether my topology 
> file of ATP molecule have something wrong? The topology file of ATP as 
> following:
> 
> ;    File '../ATP/ATP.top' was generated
> ;    By user: root (0)
> ;    On host: mjduan-desktop
> ;    At date: Wed Aug 15 16:55:53 2007
> ;
> ;    This is your topology file
> ;    "Does All This Money Really Have To Go To Char ity ?" (Rick)
> ;
> ; Include forcefield parameters
> #include "ffG43a2.itp"
> 
> [ moleculetype ]
> ; Name            nrexcl
> Protein             3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB      massB
>      1         NR      1    ATP    AN9      1       -0.2    14.0067   ; 
> qtot -0.2
>      2          C      1  60;  ATP    AC4      1        0.2     
> 12.011   ; qtot 0
>      3         NR      1    ATP    AN3      2      -0.36    14.0067   ; 
> qtot -0.36
>      4        CR1      1    ATP    AC2      2       0.36     13.019   ; 
> qtot 0
>      5         NR      1    ATP    AN1      3      -0.36    14.0067   ; 
> qtot -0.36
>      6          C      1    ATP    AC6      3       0.36     12.011   ; 
> qtot 0
>      7         NT      1    ATP    AN6      4      -0.83    14.0067   ; 
> qtot -0.83
>      8          H      1    ATP   AH61      4      0.415      1.008   ; 
> qtot -0.415
>      9          H      1&# 160;   ATP   AH62      4      0.415      
> 1.008   ; qtot 0
>     10          C      1    ATP    AC5      5          0     12.011   ; 
> qtot 0
>     11         NR      1    ATP    AN7      5      -0.36    14.0067   ; 
> qtot -0.36
>     12        CR1      1    ATP    AC8      5       0.36     13.019&# 
> 160;  ; qtot 0
>     13        CH1      1    ATP   AC1*      6        0.2     13.019   ; 
> qtot 0.2
>     14         OA      1    ATP   AO4*      6      -0.36    15.9994   ; 
> qtot -0.16
>     15        CH1      1    ATP   AC4*      6       0.16     13.019   ; 
> qtot 0
>     16        CH1      1    ATP   AC2*  & #160;   7       0.15     
> 13.019   ; qtot 0.15
>     17         OA      1    ATP   AO2*      7     -0.548    15.9994   ; 
> qtot -0.398
>     18          H      1    ATP   AH2*      7      0.398      1.008   ; 
> qtot 0
>     19        CH1      1    ATP   AC3*      8       0.15     13.019   ; 
> qtot 0.15
>     20     &# 160;   OA      1    ATP   AO3*      8     -0.548    
> 15.9994   ; qtot -0.398
>     21          H      1    ATP   AH3*      8      0.398      1.008   ; 
> qtot 0
>     22        CH2      1    ATP   AC5*      9          0     14.027   ; 
> qtot 0
>     23         OA      1    ATP   AO5*     10      -0.36  60;  
> 15.9994   ; qtot -0.36
>     24          P      1    ATP    APA     10      0.705    30.9738   ; 
> qtot 0.345
>     25         OM      1    ATP   O1PA     10     -0.635    15.9994   ; 
> qtot -0.29
>     26         OM      1    ATP   O2PA     10     -0.635    15.9994   ; 
> qtot -0.925
>     27         OA      1    ATP   O3PA &# 160;   11      -0.36    
> 15.9994   ; qtot -1.285
>     28          P      1    ATP    APB     11      0.705    30.9738   ; 
> qtot -0.58
>     29         OM      1    ATP   O1PB     11     -0.635    15.9994   ; 
> qtot -1.215
>     30         OM      1    ATP   O2PB     11     -0.635    15.9994   ; 
> qtot -1.85
>     31         OA  &# 160;   1    ATP   O3PB     12      -0.36    
> 15.9994   ; qtot -2.21
>     32          P      1    ATP    APG     12       0.63    30.9738   ; 
> qtot -1.58
>     33         OM      1    ATP   O1PG     12     -0.635    15.9994   ; 
> qtot -2.215
>     34         OM      1    ATP   O2PG     12     -0.635    15.9994   ; 
> qtot -2.85
>     ; 35         OA      1    ATP   O3PG     12     -0.548    15.9994   
> ; qtot -3.398
>     36          H      1    ATP   H3PG     12      0.398      1.008   ; 
> qtot -3
> 
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     2    gb_9
>     1   ;  12     2    gb_9
>     1    13     2    gb_21
>     2     3     2    gb_11
>     2    10     2    gb_15
>     3     4     2    gb_6
>     4     5     2    gb_6
>     5     6     2    gb_11
>     6     7     2    gb_8
>     6    10     2    gb_15
>     7     8     2    gb_2
>     7  ;    9     2    gb_2
>    10    11     2    gb_9
>    11    12     2    gb_9
>    13    14     2    gb_19
>    13    16     2    gb_25
>    14    15     2    gb_19
>    15    19     2    gb_25
>    15    22     2    gb_25
>    16    17     2    gb_19
>    16    19     2    gb_25
>    17    18     2    gb_1*   19    20     2    gb_19
>    20    21     2    gb_1
>    22    23     2    gb_19
>    23    24     2    gb_27
>    24    25     2    gb_23
>    24    26     2    gb_23
>    24    27     2    gb_27
>    27    28     2    gb_27
>    28    29     2    gb_23
>    28    30     2    gb_23
>    28    31     2 0;   gb_27
>    31    32     2    gb_27
>    32    33     2    gb_23
>    32    34     2    gb_23
>    32    35     2    gb_27
>    35    36     2    gb_1
> 
> [ pairs ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1    15     1
>     1    17     1
>    0; 1    19     1
>     2    14     1
>     2    16     1
>     5     8     1
>     5     9     1
>     7    11     1
>     8    10     1
>     9    10     1
>    12    14     1
>    12    16     1
>    13    18     1
>    13    20     1
>    13    22     1
>    14    17    0; 1
>    14    20     1
>    14    23     1
>    15    17     1
>    15    21     1
>    15    24     1
>    16    21     1
>    16    22     1
>    17    20     1
>    18    19     1
>    19    23     1
>    20    22     1
>    22    25     1
>    22    26     1
>    22    27     1
>    23    28     1
>    24    29     1
>    24    30     1
>    24    31     1
>    25    28     1
>    26    28     1
>    27    32     1
>    28    33     1
>    28    34     1
>    28    35     1
>    29    32     1
>    30    32     1
> 
> [ angles ]
> ;  ai    aj    ak funct            c0             c1            
> c2            c3
>     2     1    12     2    ga_6
>     2     1    13     2    ga_36
>    12     1    13     2    ga_36
>     1     2     3     2    ga_38
>     1     2    10     2    ga_6
>     3     2    10     2    ga_26
>     2     3      4     2    ga_26
>     3     4     5     2    ga_26
>     4     5     6     2    ga_26
>     5     6     7     2    ga_26
>     5     6    10     2    ga_26
>     7     6    10     2    ga_26
>     6     7     8     2    ga_22
>     6     7     9     2    ga_22
>     8   & #160; 7     9     2    ga_23
>     2    10     6     2    ga_26
>     2    10    11     2    ga_6
>     6    10    11     2    ga_38
>    10    11    12     2    ga_6
>     1    12    11     2    ga_6
>     1    13    14     2    ga_8
>     1    13    16     2    ga_8
>    14    13    16    0; 2    ga_8
>    13    14    15     2    ga_9
>    14    15    19     2    ga_8
>    14    15    22     2    ga_8
>    19    15    22     2    ga_7
>    13    16    17     2    ga_8
>    13    16    19     2    ga_7
>    17    16    19     2    ga_8
>    16    17    18     2    ga_11
>    15    19    16&# 160;    2    ga_7
>    15    19    20     2    ga_8
>    16    19    20     2    ga_8
>    19    20    21     2    ga_11
>    15    22    23     2    ga_8
>    22    23    24     2    ga_25
>    23    24    25     2    ga_13
>    23    24    26     2    ga_13
>    23    24    27     2    ga_4
>    25    24     26     2    ga_28
>    25    24    27     2    ga_13
>    26    24    27     2    ga_13
>    24    27    28     2    ga_25
>    27    28    29     2    ga_13
>    27    28    30     2    ga_13
>    27    28    31     2    ga_4
>    29    28    30     2    ga_28
>    29    28    31     2    ga_13
>   60; 30    28    31     2    ga_13
>    28    31    32     2    ga_25
>    31    32    33     2    ga_13
>    31    32    34     2    ga_13
>    31    32    35     2    ga_4
>    33    32    34     2    ga_28
>    33    32    35     2    ga_13
>    34    32    35     2    ga_13
>    32    35    36     2     ga_11
> 
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1            
> c2            c3            c4            c5
>     2     1    13    14     1    gd_6
>    10     6     7     8     1    gd_4
>    16    13    14    15     1    gd_14
>     1&# 160;   13    16    17     1    gd_7
>    14    13    16    17     1    gd_8
>    14    13    16    19     1    gd_17
>    14    13    16    19     1    gd_7
>    13    14    15    19     1    gd_14
>    14    15    19    16     1    gd_7
>    14    15    19    20     1    gd_8
>    22    15    19   0; 16     1    gd_17
>    22    15    19    20     1    gd_7
>    14    15    22    23     1    gd_8
>    19    15    22    23     1    gd_17
>    19    15    22    23     1    gd_7
>    13    16    17    18     1    gd_12
>    13    16    19    15     1    gd_17
>    13    16    19    20     1    gd_7
>    17    16    19    15     1    gd_7
>    17    16    19    20     1    gd_8
>    15    19    20    21     1    gd_12
>    15    22    23    24     1    gd_14
>    22    23    24    27     1    gd_11
>    22    23    24    27     1    gd_9
>    23    24    27    28     1    gd_11
>    23    24     27    28     1    gd_9
>    24    27    28    31     1    gd_11
>    24    27    28    31     1    gd_9
>    27    28    31    32     1    gd_11
>    27    28    31    32     1    gd_9
>    28    31    32    35     1    gd_11
>    28    31    32    35     1    gd_9
>    31    32    35    36     1    gd_11
>    31    32    35    36     1    gd_9
> 
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1            
> c2            c3
>     1    12    11    10     2    gi_1
>     1     2    10    11     2    gi_1
>     1    12     2    13     2    gi_1
>    60; 2     3     4     5     2    gi_1
>     2    10     6     5     2    gi_1
>     2     1     3    10     2    gi_1
>     2    11     6    10     2    gi_1
>     2     1    12    11     2    gi_1
>     2    10    11    12     2    gi_1
>     3     2    10     6     2     gi_1
>     3     4     5     6     2    gi_1
>     4     3     2    10     2    gi_1
>     4     5     6    10     2    gi_1
>     6     9     8     7     2    gi_1
>     6    10     5     7     2    gi_1
>    10     2     1    12     2    gi_1
>    13     1    14    ; 16     2    gi_2
>    13    19    17    16     2    gi_2
>    15    14    22    19     2    gi_2
>    15    20    16    19     2    gi_2
> 
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> ; Include water topology
> #include "spc.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000  & #160;    1000       1000
> #endif
> 
> ; Include generic topology for ions
> #include "ions.itp"
> 
> [ system ]
> ; Name
> Protein in water
> 
> [ molecules ]
> ; Compound        #mols
> Protein             1
> SOL               871
> 
> 
> --------------------------------
> 
> *
> 
> *
> *
> ------------------------------------------------------------------------
> *
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