[gmx-users] bad bond in polymer

[Mark Abraham]

Justin A. Lemkul wrote:
> 
> 
> nicegromacs wrote:
> 
>>   CAG -CAM
> 
> Defining a bond to a previous residue will certainly fail for at least 
> one terminus of your polymer chain.  You may find this post useful:
> 
> http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html

I don't have any relevant experience, but the quoted .rtp might be using 
a technique suited for creating a circular/infinite polymer, which would 
cause the present problem. Finite polymers need capping residues, either 
explicitly defined, or using the .tdb mechanism. See chapter 5.

Mark