[gmx-users] Cys-Cys bonding

Justin Lemkul jalemkul at vt.edu
Sat Mar 9 22:58:24 CET 2019

On 3/9/19 4:54 PM, alex rayevsky wrote:
> Dear Users and masters!
> I know that gromacs can prepare the topology with covalent bonding of
> cys-cys bridges in the individual chain on fly. However, when two different
> chains are connected with such bonds and the intital geometry is
> satisfactory (distance, angle) It doesn't work. It was done with a charmm36
> force field. I used a -ss key and renamed CYS to CYN to be sure that
> everything was taken into account. Despite the SS atontype marking for SG
> atoms in topology - nothing have changed.. this bond doesn't exist in MD....

When you have inter-chain disulfides, you need to use -merge to merge 
the relevant chains into a single [moleculetype] directive. Bonds can't 
be defined between different topological molecules.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list