Please help with following error:
“Running titrateStructureFromPDBText Service (CMIP titration)…
Service Failure.
Workflow Stopped, see program log files.”
Above error occured during AMBER and GROMACS full MD setup
Dear Shiv Gupta,
please, try to change atom names for your ligand in the input pdb, as the ones you have are too general and do not match the ones in the library (.lib). Tools adding missing atoms are trying to add all atoms from the library that are not in the structure, and so they need to match.
HETATM 1 N LIG d 1 30.114 20.024 18.847
HETATM 2 C LIG d 1 29.088 20.898 18.900
HETATM 3 O LIG d 1 29.291 22.083 18.723
HETATM 4 N LIG d 1 27.840 20.457 19.149
HETATM 7 C LIG d 1 31.472 20.505 18.578
HETATM 8 C LIG d 1 32.141 20.870 19.877
HETATM 9 C LIG d 1 31.741 20.264 21.056
HETATM 10 C LIG d 1 32.351 20.594 22.253
HETATM 11 C LIG d 1 33.366 21.529 22.277
HETATM 12 C LIG d 1 33.774 22.143 21.093
HETATM 13 C LIG d 1 33.155 21.806 19.892
HETATM 14 C LIG d 1 34.865 23.148 21.114
HETATM 15 N LIG d 1 35.875 23.188 21.996
HETATM 16 C LIG d 1 36.654 24.200 21.728
HETATM 17 N LIG d 1 36.159 24.844 20.655
HETATM 18 N LIG d 1 35.005 24.146 20.268
HETATM 20 C LIG d 1 26.726 21.406 19.204
HETATM 21 C LIG d 1 26.617 22.027 20.625
HETATM 22 C LIG d 1 25.653 21.060 21.329
HETATM 23 C LIG d 1 24.786 20.538 20.211
HETATM 24 C LIG d 1 24.705 21.752 22.309
HETATM 25 C LIG d 1 25.422 20.693 18.989
HETATM 26 C LIG d 1 23.473 20.105 20.348
HETATM 27 C LIG d 1 24.828 20.203 17.835
HETATM 28 C LIG d 1 23.564 19.637 17.971
HETATM 29 C LIG d 1 22.870 19.623 19.200
HETATM 30 C LIG d 1 22.801 20.166 21.681
HETATM 31 C LIG d 1 23.684 20.719 22.786
Please keep us informed about your progress.
Thanks for using our tool.