Hi Dr. Case,
> Antechamber can't tell you the answer. If you are near neutral pH, a
> phosphate group will certainly not be neutral. If there is a metal ion near
> to
> the phosphate in the structure, (not sure if this is true in your case),
It is true in the whole receptor-ligand structure. But because I want
to splite ligand, and ligand + Mg2+ions + receptor into two cases, I
generate a ligand pdb file containing ligand strcuture only ( no Mg2+
ions inside). However, since in the original structure that ligand
binds Mg2+ ions, the ligand charge property should consider the effect
from metal, even though until know all information in hand point that
in pH 7.0, thiamine monophosphate has +1 net charge and two hydrogen
on the phosphate group...
It seems like once metals involves in the charge calculation, it makes
things more complex. The information in crystal structure pdb could
not reliable, at least, in my case.
> there
> is even more reason to believe that the phosphate will be charged. Near
> neutral pH, you might have either the -1 or the -2 charge, depending on the
> environment in the protein. [I'm basically arguing by analogy to alkyl
> phosphates here.]
>
Besides, could you or other people could provide mopac.sh and other
modules which are necessary to run mopac.sh to me? When I followed
Junmei's suggestion to run mopac for charge calculation, mopac failed
because there was no mopac.sh in my /home/crystal/amber11/bin/ , and
indeed, there was no mopac.sh in the directory. I have no idea that
why my Amber has no mopac...
I also have another question about if using RESP is proper for the
ligand conformation that is obtained from docking. Since for RESP,
usually HF/6-31G* is used to generated charge and geometical
optimization. It seems like if I use RESP to such those ligands from
docking result, RESP will change their conformation for geometic
optimization so the ligand structure could be different from the one
in the docking result. Thus, it makes no sense if I want to use MD to
confirm the docking energy of those ligands with high scores because I
use different ligand conformation generated by RESP process.
Many thanks for your, Junme's, and forcefieldtools.org's great
assistance for my troublesome ligand and metal ion problem in advance.
Sincerely,
Crystal
> ....dac
>
>
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Received on Fri Nov 18 2011 - 17:30:04 PST
