As a beginner in gromacs,I generated an initial configuration of some peptides in mixed solvent systems. After giving pdb2gmx command for generating .gro file and .top file, an error message comes stating that residue (LIG..) couldnt be identified,its not a part of database,there is a problem with chain definition or missing terminal residues.It says that the chain does not appear to contain a recognized chain molecule. It was suggested to edit residuetype.dat. No .gro file was generated.
Some tutorials have suggested .itp files of separate solvent molecules and to #include in the force field separately as solvent molecules.
I'm not sure how to go about this whole process step by step. Please help.
Where do I modify forcefield parameters? How to generate .itp files? Should I use packmol at all or simply make use of genbox to add solvents...and how??
Hi
I never used Packmol for generating structure.
First, what you system contains?Take a careful look of your pdb files generated by packmol or etc. It has protein ligand complex then you should refer the following tut of Dr. Justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html for MD study.
The error because of residue (LIG), might be a ligand molecule so you should generate a separate topology and structure files by topology builder and later you should incorporate these files into your protein files according to the instructions given in tutorial (see the tutorial).
As far as I am concern the packmol is not a problem here. It just creates the starting pdb structure of your system. What is probably missing is the topology file (itp) of LIG part of your system. You have to create it and #include in your topol.top file.
Good luck!
Thank you everyone for your answers. Following up on your suggestions,I resolved the problem of residue identification by modifying residuetype.dat. Basically ,my system involves 'n' number of peptide molecules with say 'x' molecules of water and 'y' number of solvent molecules.
I used Packmol so that these solvent molecules could be added. I still don't have an idea of how to specify number of water molecules in my system . The feature of genbox might add specific numbers of solvent molecules if they have been specified in the database.
The problem still remains about creation of .itp files and their inclusion. I would be grateful if any of you could tell me how to create an .itp file from a coordinate file that I have. I came across a website that gives me itp files but the parameters used dont match that of the solvent model that I have.
Where do I include it in my topol.top file? Any sample documents would be highly helpful.
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