Please, I am trying to add the unit contains guanidine to the unit contains
my protein but I got
add: Argument #2 is type Unit must be of type: [molecule residue atom]
usage: add <unit/residue/atom> <unit/residue/atom>
Please, What is going wrong?
Regards,
said
On Sat, Feb 7, 2015 at 3:23 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Sat, Feb 7, 2015 at 3:16 AM, Ibrahim Said <saidibrahim569.gmail.com>
> wrote:
>
> > Dears,
> > I am sorry for confusion. x item should be a chlorine ion and when
> > calculate the charges using antechamber I got the previous prepi file.
> > Please, can I calculate the charges of guanidine and then add Cl ion in
> > xleap.
> >
>
> antechamber should only ever model single molecules, or fragments of a
> single molecule. You should never provide structures in which all atoms
> are not connected through a series of bonds to each other.
>
> Also, ions are already parametrized, so you should not include a chloride
> ion in an antechamber charge derivation. tleap can add ions (via the
> addIons command) quite easily, so you should re-run antechamber on the
> guanidine (being sure to specify the correct net charge based on the
> protonation states of each of the amine groups), and use that library when
> building a prmtop in tleap.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat Feb 07 2015 - 14:30:02 PST
