Ok! This should be straight forward but it’s driving me nuts. I haven’t done a lot of system building since earlier versions of gromacs. Now, I’m fighting with position restraints and the -r parameter in grompp.
My system topology file defines each individual component e.g.:
…lots of lipid, water and ion stuff…
#include “/home/ubuntu/DE_NOVO_PROTEINS/EPOC_0/0/Protein_A.itp”
#ifdef STRONG
#include “/home/ubuntu/DE_NOVO_PROTEINS/EPOC_0/0/STRONG_posre.itp”
#endif
[ system ]
Some name
[ molecules ]
…lipids, water and ions stuff…
Protein_A 4
The file Protein_A.itp defines the topology of a CG helix, 71 beads in length (1…71).
The file STRONG_posre.itp defines the x, y, and z position restraints of Protein_A.itp - also, 57 beads in length (1…71).
I am struggling with the wording in the documentation concerning the -r parameter from Grompp.
When using position restraints, a file with restraint coordinates must be supplied with -r (can be the same file as supplied for -c).
I will guess that when it says “can be the same file as supplied for -c” I’m assuming that’s on the condition that you are restraining all atoms/beads in the structure -c file? Surely, you can’t just supply the whole structure file of a protein, lipid and water when the generated restraint file only contains the atoms/beads for the protein?
So I’m running with my assumption that supplying grompp -r with a .gro structure file that only contains the restrained helix beads and numbered 1…71, as per its topology and its position restraint file. But, sadly, when I do that I get the following Warning:
WARNING 2 [file system.top, line 28]:
The number of atoms in
/home/ubuntu/DE_NOVO_PROTEINS/EPOC_0/0/helix_minimisation_SD.gro (71)
does not match the number of atoms in the topology (9793). Will assume
that the first 71 atoms in the topology and
/home/ubuntu/DE_NOVO_PROTEINS/EPOC_0/0/helix_minimisation_SD.gro match.
This is the command:
gmx grompp -f /home/ubuntu/DE_NOVO_PROTEINS/NPT_short_eq_STRONG.mdp -c /home/ubuntu/DE_NOVO_PROTEINS/EPOC_0/0/minimization.gro -p /home/ubuntu/DE_NOVO_PROTEINS/EPOC_0/0/system.top -o /home/ubuntu/DE_NOVO_PROTEINS/EPOC_0/0/npt_eq.tpr -maxwarn 1 -r /home/ubuntu/DE_NOVO_PROTEINS/EPOC_0/0/helix_minimisation_SD.gro
Any help is much appreciated. I’ve been on Gromacs all day and I think my eyes are getting tired.
Thanks
Anthony