[gmx-users] Re: dangling bond at at one of the terminal ends

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 4 13:44:45 CEST 2012

On 6/4/12 7:29 AM, ramaraju801 wrote:
> hi,
> i checked the .rtp file residues such as DCN,DC5,DGN,DG5,DAN,DA5,DTN,DT5
> dint have any phosphate gp but when i tested the .rtp file with a random DNA
> pdb file it is producing a topology file.

Then you'll have to translate this newfound knowledge into something useful for 
your system.  How do the .rtp entries compare to the contents of your coordinate 
file?  Is the absence of phosphate relevant?



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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