Sorry, I think it is rather simple problem to solve, but I am stuck on it.
I have 2 protein chains, so I have 2 *.itp files for them that are loaded in topol.top. What should I do to use distance restrains for protein atoms that are situated in different protein chains? There is no such problem for position restrains since I can generate it for each chain separately. But when I try to use distance restrains for atoms belonging to different chains in one user_restr*.itp file I have got atom numbers mismatch error.
Help please!
Thanks in advance!
Dear Oleg Stanislavovich Nikonov
I never did something like this, but by looking at the documentation (http://www.gromacs.org/Documentation_of_outdated_versions/How-tos/Distance_Restraints) it appears to me that distance restraints are defined in the same [molecule type], i.e. in the same .itp. Basically applying these restraints can be done only if they are inside the same molecule.
Maybe you can work with COM pulling (http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html#com-pulling) and set something like
pull-coord1-type = constraint
and define the two groups as the atoms that you want by creating some ad hoc index group.
Hope this helps,
Nicola
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