[gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Vitaly V. Chaban]

Yes. This worked even with my N2T. I will probably recreate my PDB...


On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Justin,
>>
>> Am I correct that X2TOP uses only N2T file to make a topology?
>>
>
> Yes.
>
>> I made the full line for Sulphur but it didn't change the situation.
>> It looks strange that X2TOP notices 3 bonds although I propose to have
>> 4 bonds (and they are present). If I propose 3 bonds, it readily gives
>> an output... This is like it has predefined Sulphur with 3 bonds.
>>
>
> Certainly not.  Take, for example, a simple SO4 molecule:
>
> REMARK
> HETATM    1  OAC DRG     1       5.850  14.800 -12.770  1.00 20.00
>   O
> HETATM    2  SAE DRG     1       4.810  15.780 -12.710  1.00 20.00
>   S
> HETATM    3  OAD DRG     1       3.550  15.150 -12.980  1.00 20.00
>   O
> HETATM    4  OAB DRG     1       4.770  16.390 -11.340  1.00 20.00
>   O
> HETATM    5  OAA DRG     1       5.070  16.850 -13.730  1.00 20.00
>   O
>
> The topology is generated just fine with this .n2t file:
>
> S   S   0   32.06   4   O  0.145    O   0.145   O   0.145   O   0.145
> O   OM  0   15.9994 1   S  0.145
>
> I don't know what might be going on with your system, but I would suggest
> creating an .n2t file with only entries pertinent to your system, for all
> atoms involved.  This is, of course, only really useful for debugging, since
> in theory, x2top should be easily extensible by appending the .n2t file.
>
> -Justin
>
>> Vitaly
>>
>>
>> On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban <vvchaban at gmail.com>
>> wrote:
>>>
>>> Hi,
>>>
>>> This can be the reason when X2TOP gives the following error:
>>> "
>>> Fatal error:
>>> No forcefield type for atom S (2) with 3 bonds
>>> "
>>> ?
>>>
>>> I try to translate PDB of the TFSA anion
>>>      O    O
>>>      ||     ||
>>> F3C-S-N-S-CF3
>>>      ||     ||
>>>      O    O
>>>
>>> into topology.
>>>
>>>
>>> My PDB contains optimized geometry:
>>> HEADER    TFSA
>>> COMPND    TFSA
>>> AUTHOR    VVC
>>> ATOM      1  N   TFS     1      -0.000   0.444  -0.008  1.00  0.00
>>> ATOM      2  S   TFS     1       1.401  -0.440  -0.189  1.00  0.00
>>> ATOM      3  S   TFS     1      -1.400  -0.438   0.189  1.00  0.00
>>> ATOM      4  O   TFS     1      -1.236  -1.810  -0.833  1.00  0.00
>>> ATOM      5  O   TFS     1      -1.284  -1.009   1.805  1.00  0.00
>>> ATOM      6  O   TFS     1       1.293  -1.026  -1.800  1.00  0.00
>>> ATOM      7  O   TFS     1       1.233  -1.803   0.845  1.00  0.00
>>> ATOM      8  C   TFS     1      -2.837   0.628  -0.107  1.00  0.00
>>> ATOM      9  C   TFS     1       2.836   0.630   0.105  1.00  0.00
>>> ATOM     10  F   TFS     1      -3.996  -0.097   0.093  1.00  0.00
>>> ATOM     11  F   TFS     1      -2.805   1.094  -1.408  1.00  0.00
>>> ATOM     12  F   TFS     1      -2.807   1.698   0.766  1.00  0.00
>>> ATOM     13  F   TFS     1       2.802   1.099   1.404  1.00  0.00
>>> ATOM     14  F   TFS     1       2.803   1.698  -0.771  1.00  0.00
>>> ATOM     15  F   TFS     1       3.996  -0.093  -0.093  1.00  0.00
>>> END
>>>
>>> and my n2t file is
>>>
>>> C   C   1   C               ; CNT Carbon with one bond
>>> C   C   2   C   C           : CNT double bonded Carbon
>>> O   O   1   C               ; CARBONYL OXYGEN (C=O)
>>> O   OM  1   C               ; CARBOXYL OXYGEN (CO-)
>>> O   OA  2   C   H           ; HYDROXYL OXYGEN (OH)
>>> O   OW  2   H   H           ; WATER OXYGEN
>>> N   N   3   H   C   C       ; PEPTIDE NITROGEN (N OR NH)
>>> N   NT  3   H   H   C       ; TERMINAL NITROGEN (NH2)
>>> N   NL  4   C   H   H   H   ; TERMINAL NITROGEN (NH3)
>>> N   NR5 2   C   C           ; AROMATIC N (5-RING,2 BONDS)
>>> N   NR5*    3   C   C   H       ; AROMATIC N (5-RING,3 BONDS)
>>> N   NP  3   C   C   FE      ; PORPHYRIN NITROGEN
>>> C   C       3   C   O   *       ; BARE CARBON (PEPTIDE,C=O,C-N)
>>> ; Note that order is importante here because of wildcards.
>>> C   C3  4   H   H   H   *   ; ALIPHATIC CH3 GROUP
>>> C   C2  4   H   H   C   *   ; ALIPHATIC CH2 GROUP
>>> C   C1      4   H   C   *   *   ; ALIPHATIC CH GROUP
>>> C   CB      3   C   C   C       ; BARE CARBON (5-,6-RING)
>>> H   H       1   N               ; HYDROGEN BONDED TO NITROGEN
>>> H   HO      1   O               ; HYDROXYL HYDROGEN
>>> H   HW      1   OW              ; WATER HYDROGEN
>>> H   HS      1   S               ; HYDROGEN BONDED TO SULFUR
>>> H   HC      1   C               ; HYDROGEN BONDED TO CARBON
>>> S   S       4   C  0.181  N  0.167 O 0.172  O  0.172
>>> F   F       1   C
>>>
>>>
>>>
>>> The Sulphur atoms have each 4 bonds but X2TOP wants them to have only
>>> 3. If I change the string in the N2T to 3 bonds, the topology is
>>> generated but S-C bond is absent.
>>>
>>> What can be the problem?
>>>
>>> Thanks.
>>> --
>>> Vitaly V. Chaban, Ph.D.
>>> http://www-rmn.univer.kharkov.ua/chaban.html
>>>
>>