GROMACS version: 2020.3
I have defined position restraints as described in 1UBQ tutorial on Martini webpage and simply copied the steps over to my own protein, an IgG.
But after running energy minimization, the protein structure is destroyed.
Is there something that ive missed out or should i be adding more restraints?
Picture of the protein here:
imgur.com/grjq2Ot
Just curious, do typical gromacs restraint options work in the same way for martini models?
Anything in particular that i should be taking note of or changing to suit a martini model?
Position restraints do not seem to be restraining the backbone properly.
Copied from the protein.itp file:
#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
1 1 POSRES_FC POSRES_FC POSRES_FC
3 1 POSRES_FC POSRES_FC POSRES_FC
5 1 POSRES_FC POSRES_FC POSRES_FC
… … …
This looks different from the typical position restraints of all-atom models.
It seems that the force constant can be defined but im not sure what the syntax really means.
If i used define = -DPOSRES in .mdp file, will it make POSRES_FC = 1000 or 0 ?
Are you sure the protein is being destroyed and not just appearing to cross periodic boundaries? Can’t really tell from that picture.
It should be 1000 if not defined, and you definitely need the -DPOSRES
yes it seems that bonds are much longer than it should be.
If not defined, it will be 1000? Wouldnt that mean if i used define, there’d be a restraint?
Here are some zoomed-in screenshots.
Highlighted bond is really long here.
This is the middle of the IgG, supposedly the somewhat symmetrical-looking part but it has been broken in two.
Original structure should look like this. Bonds are not connected here because of the modeling software im using. I only know how to add in CONECT records from trajectories but this is from the first conversion of all-atom to martini model.
Right but bonds can appear stretched if one atom is poking through the box boundary, when in reality they’re fine. Minimization really shouldn’t move atoms much at all - really small adjustments. Have you visualized the trajectory video? Is everything breaking apart at once or moving over time? What visualizer are you using? In VMD you can duplicate the box in the x/y/z dimensions and that can make it clearer, or you can run gmx trjconv to put everything together.
RE the position restraints - #ifdef should be interpreted as “if defined”, #infndef is “if not defined”, so:
means - if POSRES is defined, and POSRES_FC is not defined, set POSRES_FC to 1000.
These were the commands i input.
gmx grompp -p beva.top -r solvated_neutralized.gro -c solvated_neutralized.gro -f minimization.mdp -o minimization.tpr
gmx mdrun -deffnm minimization -v
gmx trjconv -s minimization.tpr -f minimization.trr -o minimization_traj.pdb -pbc whole -conect
The last command should be putting the molecule together in one piece if its due to PBC.
Im currently using SAMSON software since ive been more familiar with it. I did try to familiarize with VMD previously but i couldnt understand how to operate it, much less visualize martini models in it.
It seems that from the very first image of trajectory, the structure is already broken up.
One question, i know editconf can add CONECT records into .gro files to produce .pdb files. Can this be done for martini models as well? From documentation, the topology is required for this. How should i include topology for this command? The manual doesnt state another file type (e.g. .top) to include in the command.
