[gmx-users] add a group to an amino acid

Wed Nov 17 04:27:35 CET 2010

On 16/11/2010 9:04 PM, hengame fallah wrote:
> Thank you very much, Mark!
> Now i have errors from my .top file after grompp command.
> The question is that why in pdb2gmx, editconf ,genbox and make_ndx 
> steps i don't see these errors:
>
> ...
> processing topology...
> Opening library file /usr/share/gromacs/top/ffoplsaa.itp
> Opening library file /usr/share/gromacs/top/ffoplsaanb.itp
> Opening library file /usr/share/gromacs/top/ffoplsaabon.itp
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
>
> ERROR 1 [file topol.top, line 412]:
>   No default Angle types
>
>
> ERROR 2 [file topol.top, line 567]:
>   No default Ryckaert-Bell. types
>
>
> ERROR 3 [file topol.top, line 570]:
>   No default Ryckaert-Bell. types
>
>
> ERROR 4 [file topol.top, line 573]:
>   No default Ryckaert-Bell. types
>
>
> ERROR 5 [file topol.top, line 580]:
>   No default Ryckaert-Bell. types
>
>
> ERROR 6 [file topol.top, line 581]:
>   No default Ryckaert-Bell. types
>
>
> ERROR 7 [file topol.top, line 582]:
>   No default Ryckaert-Bell. types
>
> Opening library file /usr/share/gromacs/top/spc.itp
> Opening library file /usr/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 1 [file topol.top, line 664]:
>   System has non-zero total charge: 6.000000e-02

0.06 means your residue's charges do not add to zero, and they should.

>
>
>
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
>
> There was 1 note
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: ../../../../src/kernel/grompp.c, line: 986
>
> Fatal error:
> There were 7 errors in input file(s)
>
> *topol.top:*
> ...
> 43   opls_238      3    BOC N       17       -0.5    14.0067   ; qtot 0.5
>     44   opls_241      3    BOC      H       17        0.3      
> 1.008   ; qtot 0.8
> 45   opls_283      3    BOC CA      17       0.04     12.011   ; qtot 0.84
> 46   opls_140      3    BOC HA1     17       0.06      1.008   ; qtot 0.9
> 47   opls_140      3    BOC HA2     17       0.06      1.008   ; qtot 0.96
> 48   opls_149      3    BOC CB     18      0.055     12.011   ; qtot 1.015
>     49   opls_140      3    BOC     HB     18       0.06      1.008   
> ; qtot 1.075
>     50   opls_145      3    BOC    CG1     18     -0.115     12.011   
> ; qtot 0.96
>     51   opls_145      3    BOC    CD1     19     -0.115     12.011   
> ; qtot 0.845
>     52   opls_146      3    BOC    HD1     19      0.115      1.008   
> ; qtot 0.96
>     53   opls_145      3    BOC    CD2     20     -0.115     12.011   
> ; qtot 0.845
>     54   opls_146      3    BOC    HD2     20      0.115      1.008   
> ; qtot 0.96
>     55   opls_145      3    BOC    CE1     21     -0.115     12.011   
> ; qtot 0.845
>     56   opls_146      3    BOC    HE1     21      0.115      1.008   
> ; qtot 0.96
>     57   opls_145      3    BOC    CE2     22     -0.115     12.011   
> ; qtot 0.845
>     58   opls_146      3    BOC    HE2     22      0.115      1.008   
> ; qtot 0.96
>     59   opls_145      3    BOC     CZ      23          1     12.011   
> ; qtot 1.96
>     60   opls_264      3    BOC     Cl        23         -1     
> 35.453   ; qtot 0.96
> 61  opls_224B     3    BOC CG2     24      -0.12     12.011   ; qtot 0.84
> 62   opls_140      3    BOC HG1     24       0.06      1.008   ; qtot 0.9
> 63   opls_140      3    BOC HG2     24       0.06      1.008   ; qtot 0.96
> 64   opls_271      3    BOC C       25        0.7     12.011   ; qtot 1.66
>     65   opls_272      3    BOC     O1     25       -0.8    15.9994   
> ; qtot 0.86
>     66   opls_272      3    BOC     O2     25       -0.8    15.9994   
> ; qtot 0.06
> ...
> [ angles ]
> ...
> line 412: 45    48    61     1
> ...
> [ dihedrals ]
> ...
> line 567: 43    45    48    61     3
> ...
> line 570: 46    45    48    61     3
> ...
> line 573: 47    45    48    61     3
> ...
> line 580: 45    48    61    62     3
> line 581: 45    48    61    63     3
> line 582: 45    48    61    64     3
> ...
>
> it seems that "45   48    61" is the problem. CA    CB    CG2
> Where i should define angle type for it?

Those three atoms have types. The type of function to put on an angle 
whose three atoms have given types is defined in the force field. 
Evidently, there isn't one for the types of these atoms. This relates to 
choosing your atom types properly, like I've said twice before now. Go 
and look up their types in the .rtp, and then look up in the .atp  what 
environments the types for which they were parameterized, and see what 
your non sequitur is.

Mark
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