normal Protein breaking up with extended bonds

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3 years 11 months ago - 3 years 11 months ago #8645 by darrenphua
Protein breaking up with extended bonds was created by darrenphua
I have defined position restraints as described in 1UBQ tutorial 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.
Last edit: 3 years 11 months ago by darrenphua.

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3 years 11 months ago #8647 by riccardo
Replied by riccardo on topic Protein breaking up with extended bonds
(3D, I guess) positions restraints should fix the coordinates of your proteins to the initial value. They must work with Martini too, so you must be doing something wrong with the command. Please check carefully the Gromacs manual.

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3 years 10 months ago - 3 years 10 months ago #8651 by darrenphua
Replied by darrenphua on topic Protein breaking up with extended bonds
Ah that might be the reason. I do not find any position restraint file or portion anywhere. Does the martini script produce posres.itp? Or do i have to manually create it using coordinates of the martini model?

EDIT:
I found a position restraint segment in 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, whereby numbers are described in the table.
Is there anything different that i should be doing with martini models?
I have added define = -DPOSRES into .mdp file so im not sure why its not working out.
Last edit: 3 years 10 months ago by darrenphua.

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