i am working with MD simulations. i am facing error from CGenff server while predicting topology for my ligand file ligand_fix.mol2. error= "readmol2 warning: unrecognized element "Du"readmol2 warning: unrecognized element". can anyone please suggest me any solution to fix this problem ?
ok Martin Klvana sir thank u for your valuable answer but, let me know is there any way to fix this problem ?
Subodh Choukidar, edit the mol2 file: assign correct element to each atom.
ok Martin Klvana sir thank u again for your reply, i solved the error of Du element using discovery studio.
but, i am now facing error like : "readmol2 warning: non-unique atoms were renamed. Now processing molecule clexane ... attype warning: oxonium ion not supported; skipped molecule".
could you please guide me for this ?
The "clexane_fix.mol2" file looks muddled up (see the attached snapshot from PyMOL). What i would do:
1. Download two-dimensional (2D) SDF file of clexane from PubChem: https://pubchem.ncbi.nlm.nih.gov/substance/349990081
2. Convert 2D SDF file to 3D SDF file in KNIME (SDF Reader >>> 3D Coordinates >>> SDF Writer >>> clexane.sdf) or using ChemAxon's molconvert command-line program.
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