[gmx-users] inserting new residue

[Erik Lindahl]

On Thursday, January 23, 2003, at 08:19  AM, sadhna wrote:

>
> hi,
>     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 
that

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.

Cheers,

Erik