I am try to convert the .pdb file of hydroxyapatite into .gro and ormat using the command pdb2gmx. I have tried all possible force field but all are giving the same error i.e. "Fatal error: Residue 'MOL' not found in residue topology database". How can i fix this problem?
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Most force fields will support Ca2+ ions (but they should not be called MOL), so you have to add specific residue definitions for phosphate and hydroxide (again, giving specific residue names).
You can use PRODRG to convert a small molecule pdb file into gro file and it also write de itp file
The URL of PRODRG server is http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/
An example of how to use PRODRG with GROMACS for Protein-ligand complex is in http://www.dddc.ac.cn/embo04/practicals/9_15.htm
IIRC, PRODRG does not support Ca2+ and moreover there is no reason to try to generate a topology for ions with known parameters. Perhaps even more relevant is the fact that PRODRG generates very low-quality topologies that have to be extensively corrected before they should be used in simulations.
list the MOL in .rtp and atomtypes and bonded/nonbonded interactions in respective files in forcefield.ff folder
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