Servers for ligand topologies/parameters

How to generate topology/parameter files for unknown ligand

What is meant here by unknown ligand is that it is not found in the standard monomer library in CCP4 or on the HIC-Up website.

You also might want to check the NCBI Pubchem database at http://pubchem.ncbi.nlm.nih.gov/. The sdf file can be downloaded and converted to PDB format.

There is excellent solution to this problem, and it is found on Dundee PRODRG server. It is quite self-explanatory (you define the ligand structure by providing coordinates in PDB format, drawing molecule using JME editor, etc.) and produces coordinates and topology/parameter descriptions in the following formats:

- PDB

- SYBYL2

- MDL Molfile

- GROMACS

- AUTODOCK

- WHATIF

- HEX

- LIGTOR

- CNS

- REFMAC5

- O

- SHELX

One inconvenience is that PRODRG server always names your new residue DRG and gives atoms some funny names (CAA, CAX, etc.). If you prefer to control the naming system, take the PDB output, rename residue/atoms to your liking and rerun it.

base pairing and base stacking

- PDB coordinates to Restraints - This Web-server generates custom RNA/DNA base stacking and base pairing restraints for crystallographic refinement. Input is in PDB format. Output is Pymol , CNS and PHENIX formatted.