Depending on your end goal, you might also want to use the "crosslink"
command rather than "bond". "Bond" only makes a single bonding interaction
between the two specified atoms, whereas "crosslink" makes the bond, all
angles, and all dihedral angles according to the rules listed in your .prep
file.
On Thu, Sep 15, 2011 at 11:51 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Sep 14, 2011, Fabrício Bracht wrote:
>
> > Hi. I am trying to make a bond between two atoms using xleap as part
> > of a parameterization process for a new aminoacid residue. I have both
> > my protein and new residue in the same pdb file. I am using ambertools
> > 1.5. Every time I hit the bond command, It gives out an error message.
> > Here are some details on my atom numbering.
> > The first atom is Atom number 1519. It ts a carbonyl carbon (C) in
> > residue 104. This should be linked to atom number 59082 wihin residue
> > 3178 (N1). I've called the molecule in leap "mic".
>
> bond mic.104.C mic.3178.N1
>
> Note that you can use the "desc" command to see if each individual part is
> what you want, e.g.
>
> desc mic.104.C
>
> should show details of that atom, including what it is currently bonded to.
> After the "bond" command, repeating the desc command should show the new
> bond.
>
> ...good luck...dac
>
>
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Received on Thu Sep 15 2011 - 17:30:04 PDT
