I have this error:
"Fatal error:
Residue 'UNK' not found in residue topology database"
My residue UNK is Digalactosylodiacylglicerol. I use OPLS-AA force field. I created topology of my residue by using LigParGen http://zarbi.chem.yale.edu/ligpargen/. How to add this residue to topology database?
I want to build my DGDG membrane from scratch and I need to create topology.
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
However, if you already have a topology, there's no reason to run pdb2gmx or alter the .rtp file. The job of pdb2gmx is to produce a topology, but you already have one.
I guess you want to perform MD for Protein-Ligand complex. If so, you might need to follow this tutorial to generate UNK topologies http://www.mdtutorials.com/gmx/complex/index.html
please follow this tutorial to generate UNK topologies http://www.mdtutorials.com/gmx/complex/index.html . may be this will solve your problem.
I can generate .gro and itp files from the LigParGen. However it is very confusing use them. I understand usning a .pdb file and inserting a new ligand .rtp file in oplsaa.ff, the running gmx pdb2gmx -f xxx.pdb.
It seems easier to use the LigParGen server to generate required information. However, it is very unclear how to use the itp and gro files. Based on the internet, I tried a few things but I'm feeling my way in the dark. Can anyone help?
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