Difference between revisions of "Servers for ligand topologies/parameters"

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== How to generate topology/parameter files for unknown ligand ==
 
== 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.
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CCP4 AceDRG ([http://www.ccp4.ac.uk/dist/checkout/acedrg/doc/Manual.pdf]) needs to be fed the SMILES string of your compound, and it returns the CIF file.
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Many compounds are actually already in the CCP4 dictionary. Finding out whether a compound is, is a two-step procedure:
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# Go to http://ligand-expo.rcsb.org/ and use the search option to find out whether the compound is already in the PDB
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# If it is, you now have a residue name. To check whether the compound is also in the CCP4 dictionary, just use the 'Get monomer' option in [[Coot]].
  
You also might want to check the NCBI Pubchem database at http://pubchem.ncbi.nlm.nih.gov/
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Within coot, you can
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* use Lidia to make a chemical diagram, press "Apply" to run Acedrg
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* or use Lidia to determine the SMILES string and use the "Make a Ligand" task in CCP4i2
  
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:
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You also might want to check the [http://xray.bmc.uu.se/hicup/ HIC-Up] website, and the NCBI Pubchem database at http://pubchem.ncbi.nlm.nih.gov/. The sdf file can be downloaded and converted to PDB format.
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Another solution to this problem is the [http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ Dundee PRODRG server]. It is 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]  
 
- [http://www.rcsb.org/ PDB]  
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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.
 
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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== base pairing and base stacking ==
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- [http://rna.ucsc.edu/pdbrestraints/ 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.

Latest revision as of 07:47, 11 July 2018

How to generate topology/parameter files for unknown ligandEdit

CCP4 AceDRG ([1]) needs to be fed the SMILES string of your compound, and it returns the CIF file. Many compounds are actually already in the CCP4 dictionary. Finding out whether a compound is, is a two-step procedure:

  1. Go to http://ligand-expo.rcsb.org/ and use the search option to find out whether the compound is already in the PDB
  2. If it is, you now have a residue name. To check whether the compound is also in the CCP4 dictionary, just use the 'Get monomer' option in Coot.

Within coot, you can

  • use Lidia to make a chemical diagram, press "Apply" to run Acedrg
  • or use Lidia to determine the SMILES string and use the "Make a Ligand" task in CCP4i2

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

Another solution to this problem is the Dundee PRODRG server. It is 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 stackingEdit

- 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.