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.i...@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
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