[gmx-users] bad bond in polymer

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 13 06:03:42 CEST 2009

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.


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