How to convert pdb files to sdf ?

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MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

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MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

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fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

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fatal error

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fatal error

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fatal error

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Nicolas Panel

Open Babel should do the job (http://openbabel.org/wiki/Main_Page). It can convert molecular structures form one format to another (including sdf).

PyMol is also able to convert a pdb to sdf format.

Jürgen Wintner

"Easy Convert" http://biochemlabsolutions.com/Molecule%20Docking/FORMATS/Formats%20PDB%20PDBQT%20SDF%20MOL.html

https://cactus.nci.nih.gov/translate/

Md. Mahbubur Rahman

The above-mentioned solutions should work. I am just adding another one.

You can convert file format by BIOVIA Discovery Studio also. It worked great for me.