Servers for ligand topologies/parameters: Difference between revisions
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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. | 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. | ||
You also might want to check the NCBI Pubchem database at http://pubchem.ncbi.nlm.nih.gov/ | 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 [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: | 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: | ||
Revision as of 22:18, 25 June 2008
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.