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 - 05:30:02 PST
