I have a pdb file that contains DPPC molecules and other molecules. I want to generate .gro and .top files from this pdb file using the Gromacs command pdb2gmx. I am trying to use the Charmm36 force field (update jul20), which contains atomistic topologies for DPPC.
The problem is the DPPC atom names in my pdb file are not being recognized - i.e. Fatal error: Atom N4 in residue DPPC 1 was not found in rtp entry DPPC with 130 atoms while sorting atoms.
Is there a way around this? Maybe I need to put the pdb file together in another way or use a different force field.
Any suggestions would be appreciated.
Dear Douglas Diehl
Pdb2gmx command generates topology for protein, not for lipids.
you could find itp file for lipids in this link
http://wcm.ucalgary.ca/tieleman/downloads
Also, this tutorial helps you in bilayer simulation
http://www.mdtutorials.com/gmx/membrane_protein/index.html
Hope it helps
Hi Douglas! In order to get the correct file you shall see in the force field folder the file named as lipids.rtp. There you can search for DPPC. In the residue you may see the order they used when they were drawing the molecule, names of atoms , bonds between them. According to that rtp-description of the residue you can simply draw your molecule and name atoms in exactly the same way. Another alternative is to use online Charmm-Gui. It will generate you topologies for gromacs-software.
Pdb2gmx , in principle, can generate you topologies for any desired molecule. All what you need is to add it to rtp-residues and sure that all force field parameters exist in the desired force field.
Inna Ermilova One more question. How does one draw the molecule and name the atoms in the same way as the rtp-description? For example, what program can be used to do this? I am a bit new to this.
Dear Douglas, you can draw it using, for example, Avogadro (free of charge). There before you draw you use "label": it will show you order of atoms then. Save it as pdb. Then when you are done with drawing, open pdb-file in text editor and rename atoms as well as residue. The residue is normally automatically named as LIG or UNK in Avogadro, you need it to be DPPC. Also renaming save the right amount of spaces between symbols, or the file won't be readable for gromacs. You can also use Geany text editor. There you can replace columns of names from one file to another. Hope it helps. 😊
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