Hello everyone,
I’m trying to apply a distance restraint between two atoms of a peptide, Chain A and Chain B. The issue is that both
Chain A and Chain B have the same numbering in the topology
, i.e., 1-300 atoms (they are identical peptides). I need to keep the terminal patches, so I can’t merge them into the same chain. Is there any way to specify that the atoms I need to restrain are from Chain A and Chain B?
Any suggestions are highly appreciated.
Dear @scinikhil ,
Sorry I didn’t understand, do you want to restrain one atom of Chain A with respect to one atom of Chain B or you do want to restrain two atoms -one with respect to the other in the same chain - in Chain A and similar in Chain B?
Anyway, the best way to go that will always work is to use the pull module, where you can specify the groups you refer to and restrain them!
@obZehn i need to apply distance restrain to few atoms from Chain A to (lets say 2, 4, 5, 60 ) to atoms of Chain B (2, 4, 5, 60). so 2-2, 2-4,5-5 (no need to be same atoms). Im aware of pull module but looking for a suggestion to see any other options.
Then I can’t help you, sorry. For these type of restraints I would use or the topology of the molecule (but you can’t as they are atoms in different topologies) or the pull code. Maybe there is some fancy way to add some kind of interaction type in the force field, but here I leave space to more expert people. I would still suggest to use the pull code though, as it seems by far the most bullet proof approach! Simple to debug, implement, and interpret.
@obZehn Thanks