GROMACS version: 2020, 2018
GROMACS modification: Yes/No
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I am trying to simulate a system with 4 identical proteins and restrain the C-Alpha of each of them (there are also some small molecules in the box too), so that the proteins wouldn’t unfold during the thermal annealing stage. I found few discussions on the subject (i.e. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-July/099219.html), and tested it on small molecules, and it worked just fine. Nevertheless, for proteins the very same approach doesn’t seem to work.
Say, I have the following system:
#include “Protein2.itp”; exactly the same as Protein1, except the molecule type name
#include “Protein3.itp”; exactly the same as Protein1, except the molecule type name
#include “Protein4.itp”; exactly the same as Protein1, except the molecule type name
#include “API2.itp”; exactly the same as API1, except the molecule type name
[ system ]
Protein with API
[ molecules ]
; Compound #mols
If I make some 5 APIs restrained (and specify it in the API.itp [ position_restraints ] section) and keep the original topology of the other 5, everything works well. Also, if I restrain only the Protein1 it works also fine. However, if I try to restrain Protein1 and Protein2 (either as two different types of files Protein1.itp + restr_Protein1.itp and Protein2.itp + restr_Protein2.itp, or as “Protein1 2”) it either explodes with segfault, or says:
Condition: type_max - type_min + 1 == dd->nres
All distance restraint parameter entries in the topology should be consecutive.
As it works fine for smaller molecules and even 1 restrained Protein plus several restrained APIs, I assume it has something to do with the numbering of the residues for the protein (which has 153 amino acids).
I would be extremely grateful if someone could help with a hint on how to set up intra-protein distance restraints properly for all 4 molecules.