[gmx-users] Cys-Cys bonding

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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