[gmx-users] Atom type SDMSO not found

[Sun Iba]

Here is the generated topology of ligand with PRODRG server, i believe
something is wrong with atom typs here;

 PRODRG COORDS
   29
    1UNK  CLAW     1   1.328  -0.638  -0.151
    1UNK  CAM      2   1.384  -0.765  -0.049
    1UNK  SAU      3   1.520  -0.861  -0.089
    1UNK  CAG      4   1.503  -0.954   0.053
    1UNK  CLAV     5   1.606  -1.085   0.095
    1UNK  CAN      6   1.396  -0.913   0.128
    1UNK  HAR      7   1.368  -0.958   0.223
    1UNK  CAO      8   1.327  -0.803   0.069
    1UNK  SAT      9   1.181  -0.728   0.145
    1UNK  OAR     10   1.144  -0.805   0.261
    1UNK  OAS     11   1.215  -0.589   0.171
    1UNK  NAQ     12   1.058  -0.732   0.029
    1UNK  HAS     13   1.052  -0.655  -0.035
    1UNK  CAC     14   0.963  -0.835   0.018
    1UNK  CAD     15   0.837  -0.802  -0.035
    1UNK  HAD     16   0.817  -0.699  -0.065
    1UNK  CAE     17   0.739  -0.899  -0.051
    1UNK  HAE     18   0.642  -0.870  -0.093
    1UNK  CAB     19   0.987  -0.969   0.051
    1UNK  HAB     20   1.085  -0.998   0.090
    1UNK  CAA     21   0.887  -1.065   0.036
    1UNK  HAA     22   0.908  -1.168   0.066
    1UNK  CAF     23   0.759  -1.034  -0.015
    1UNK  NAP     24   0.657  -1.133  -0.031
    1UNK  CAH     25   0.519  -1.090  -0.064
    1UNK  CAI     26   0.421  -1.196  -0.011
    1UNK  CAJ     27   0.447  -1.336  -0.069
    1UNK  CAK     28   0.595  -1.359  -0.104
    1UNK  CAL     29   0.690  -1.276  -0.016
   1.33540   1.33540   1.33540

The atom types look strange to me. Please help

On Wed, Jul 29, 2015 at 10:18 AM, su <sun.iba2 at gmail.com> wrote:

> Hello everyone
> I am doing protein-ligand simulation according to Justin's tutorial. After
> running gmx grompp command, i encountered following error:
> Fatal error:
> Atomtype SDMSO not found.
> Is this the force field matching problem? because i am not able to find
> out any such atom types in any of the generated files.
> Please guide me where the problem is. All other commands ran properly.
>
> Suniba
> Sent from my iPhone