[gmx-users] Re: minimize multi-chain protein

[amit.oberai at yale.edu]

HI,

I am using gromacs for energy minimization.  Can anyone advise me on how to do
this for a multi-chain protein.

When I try to minimize a protein with multiple chains, gromacs creates a bond
between the last residue of the previous chain and the first residue of the
next chain, not recognizing they are in separate chains.

My pdb file has distinct chain names for all the different chains.

Thanks!
Amit