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New page: == 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 [http://x...

== 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 [http://xray.bmc.uu.se/hicup/ HIC-Up] website.

There is excellent solution to this problem, and it is found on [http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ Dundee PRODRG server]. It is quite self-explanatory (you define the ligand structure by providing coordinates in PDB format, drawing molecule using [http://www.molinspiration.com/jme/ JME editor], etc.) and produces coordinates and topology/parameter descriptions in the following formats:

- [http://www.rcsb.org/ PDB]

- SYBYL2

- MDL Molfile

- [http://www.gromacs.org/ GROMACS]

- [http://autodock.scripps.edu/ AUTODOCK]

- WHATIF

- [http://www.csd.abdn.ac.uk/hex/ HEX]

- LIGTOR

- [http://cns-online.org/ CNS]

- [http://www.ysbl.york.ac.uk/~garib/refmac/ REFMAC5]

- [http://xray.bmc.uu.se/alwyn/ O]

- [http://shelx.uni-ac.gwdg.de/SHELX/ 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.
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