I have a molecule that i want to simulate using gromacs. As i tried pdb2gmx, there is no error in the console, but the topol file did not record any [moleculetype] datas. It did not hinder the MD when i tried to proceed with em and so on, but im curious of the difference in topol generation.
I am using charmm36 jul2021 ff and included heteroatom cu2p.
I'll include the topol file generated as well as other topol file which has [moleculetype] data in it as comparison.
Thanks in advance
Talia Serseg, there is no error detected by gromacs seeing the console log not giving any error. The gro file was built correctly and all, but the topology file did not have posre, [atom] [molecule]. Usually thee would be atoms location recorded inside the topol file. I'll include my previous md topol file as comparison.
Jonathan Purnomo
The difference is that the file 'topol.top' has the following statements
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Other_chain_B.itp"
while the file 'topol(1).top' does not.
In principle you have two ways to prepare your topology, which are both correct. One option is to write everything in the topology file, which is the approach of file topol(1).top for the chain of interest. This means that the chain is fully defined in the file, that is it has the sections
[molecule_type]
...
[atoms]
...
[bonds]
...
etc
The second approach is to put all these sections in a separate .itp file and include them in the topology with the #include statement.
The approaches are equivalent, that's why you get no errors and both do work. The difference is the readability of the topology. The file 'topol(1).top' is long and hard to read. Compare instead with 'topol.top', which excluding the comments reads simply as
#include "./charmm36-jul2021.ff/forcefield.itp"
#include "topol_Protein_chain_A.itp"
#include "topol_Other_chain_B.itp"
#include "./charmm36-jul2021.ff/tip3p.itp"
#ifdef POSRES_WATER
[ position_restraints ]
1 1 1000 1000 1000
#endif
#include "./charmm36-jul2021.ff/ions.itp"
[ system ]
Protein
[ molecules ]
Protein_chain_A 1
Other_chain_B 1
that is include forcefield parameters, include the topology for protein A and chain B, include topology for tip3 water model and define the constraints on its oxygen atom if requested with 'POSRES_WATER', and include parameters for ions. The name of the system is 'Protein' and is composed by 1 protein A and 1 chain B.
If you wrote the full list of parameters rather than
#include "./charmm36-jul2021.ff/forcefield.itp"
and the full list of parameters (like in the topol(1).top file) for the chains and then the parameters for water and ions rather than
#include "./charmm36-jul2021.ff/tip3p.itp"
#include "./charmm36-jul2021.ff/ions.itp"
you would end up with a .top file several thousands lines long which would be hard to read and, consequently, very error prone, especially since the topology entries need to have a very precise order both in the molecule definitions and in their call order. The approach of breaking in .itp files and including them with #include statements makes so that the topology can be very easy to read and to debug, plus it's just overall easy to manage if anything need to be added and/or removed.
Hope this helps,
Nicola
- Badges
- Science topic
- Similar topics
- Filing