One thing which you could do is to write your three proteins into one
molecule definition (if you use .itp files, then make one .itp for all
three). Then at the end of the molecule definition you can add the
constraints.
To merge the three proteins is rather easy but cumbersome, you must
shift all the atom numbers of the second and third protein. So if each
protein would have 100 atoms, protein2 would start with atom 101.
depending how big your proteins are it could be better to write a script
which merges the three proteins instead of doing it by hand.
Greetings
Thomas
Hi everyone. ?I'm doing a simulation of a protein aggregate with 3 proteins.
?Ideally, I would like to constrain the distance between the center of mass of
peptide 1 and the COM of peptide 2, and also constrain the distance between the
combined COM of peptides 1 & 2, with the COM of peptide 3. ?The pull code only
allows constraints between the reference group and other groups, as far as I know.
Using constraints in the topology only allows constraints between atoms, not
COM's. ?This is not ideal for me, but might be acceptable. ?However,
constraints are only allowed within a single molecule.
Does anyone know how to deal with this problem? ?Thanks a lot.
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