[gmx-users] Atom type SDMSO not found

[Justin Lemkul]

On 7/29/15 12:59 AM, Sun Iba wrote:
> 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

Probably because those aren't atom types (they are names) and this isn't a 
topology (it's a coordinate file).

-Justin

>
> 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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================