Sequence of atoms in .itp and .pdb

User discussions
1

When i am using a .itp file created by SwissParam for a small molecule, or even for other molecules with other topology generators for example, are atom numbers important?

To give more detail, i’m referring to atom numbers found in .itp file image versus atom numbers found in .pdb file

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In order for GROMACS to use the .itp file properly, i know that atom names must be the same as those in .pdb.
But comparing both files, the sequence of atoms is different. If i were to copy atom names over from .itp to .pdb, do i also have to rearrange the lines such that atom 1 in .itp is the same as atom 1 in .pdb?

2

The atom names and their order of appearance must match what is in the topology.

3

Got it! Just found out that for some topology generators, they also generate pdb or gro files. And I should be using them instead of my original pdb files. Otherwise, atom sequences wouldn’t match. Thanks!

4

I am having the same problem. Will you please let me know, how to resolve it?
I am trying to simulate Dmpc lipid bilayer, but the sequence of atoms in pdb mismatches with dmpc.itp.