GROMACS version: 2023
GROMACS modification: No
Hi everyone, this is my first time posting here :)
I downloaded gromacs 2023 today and I’ve been going through the tutorial I found here: Lysozyme in Water
In the first step of the tutorial, we use pdb2gmx to produce the topology, position restraint, and post-processed structure files. This is the command:
gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce
A file, posre.itp was generated with the position restrains but wouldn’t be relevant until the equilibration part of the tutorial. I got through the system creation and minimization fine.
When I got to the equilibration part of the tutorial, Lysozyme in Water, it recalls the posre.itp file and implies that we’re going to use it but the next command is
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
which fails with the output:
WARNING 1 [file topol.top, line 33879]:
The following macros were defined in the ‘define’ mdp field with the -D
prefix, but were not used in the topology:
POSRES
If you haven’t made a spelling error, either use the macro you defined,
or don’t define the macro
Program: gmx grompp, version 2023
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 638)
Fatal error:
No molecules were defined in the system
From the docs on grompp, the -r is for the position restraints but I’m not passing posre.itp to grompp at all here, in fact grompp will refuse to take an itp file with the -r flag. I thought this might be a typo in the tutorial? I looked at the very first topology file generated by pdb2gmx and it includes blocks at the end for including posre.itp and other system properties. All subsequent topology files, which were given as inputs to solvate, grompp, and genion (in that order), retained this appended section at the end. However, the topology file that I am left with after minimizing with
gmx grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em
lacks these include blocks. Running grompp with topol.top in previous steps did not erase these blocks, so I’m guessing that the output of mdrun was a topology that lacked them.
How can I get this information to be retained after minimization in the topology file or how can I use the mdrun generated topology file in conjuction with the pdb2gxm generated itp file?
Thank you! Any and all help is appreciated!
Summary of what I’ve done:
gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce
gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -neutral
gmx grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em
gmx energy -f em.edr -o potential.xvg
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
^ Failure