[gmx-users] inserting new residue
lindahl at stanford.edu
Thu Jan 23 06:55:25 CET 2003
On Thursday, January 23, 2003, at 08:19 AM, sadhna wrote:
> I have inserted a new residue in the residue toplogy file. Gromacs
> accepts it but the problem is when i see it in web lab viewer it shows
> single bond for carbonyl oxygen(of the peptide bond) instead of double
> bond .
> Where could i have gone wrong?
I'm not sure what you mean by single vs. double bond in the viewer; a
"double bond" in Gromacs (and other MD programs) is just a normal bond
1) is slightly shorter
2) has a higher force constant
3) has a dihedral to keep the group planar (if necessary)
So, normally it will just look like a normal bond in a viewer.
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