Dear Dr. Case,
Thank you for your information. Since the local machine I am using has
trouble to install MOPAC 7 or 6 (suggested by Junmei), and WebMO due to
graphic card, I just think if Amber 11 has its own mopac but just fail to
install during Amber installation, someone maybe has some ideas to help me.
For RESP on RED, I have a concern that if RESP charge calculation is proper
for my ligand. I saw the tutorial (Hands on tutorial 4, Using Antechamber
to Create Leap Input Files...) and knew a step called geometry
optimization. This step seems to change conformation of ligands. I want to
know how great the conformation changes during RESP charge calculation, and
if this conformational change will be recorded into mol2 file, and used by
xleap to handle the parameters of my ligand and further MD simulation.
Why I have such that concern is because for my case, my ligand conformation
is obtained by the docking, and the purpose of my MD simulation is to
validate the virtual screening results. If RESP generates charge by
changing the docking conformation, and the changed conformation must be
used in xleap and MD, it makes my validation inconsistent because I use
different conformation in MD. I understand RESP seems an alternative way to
generate charge. Francisco also showed me the RESP result for my weird
ligand. However, considering the restriction of my case, I have make sure
whether the conformation change affects my validation to docking results
with MD. Once I confirm the conformation change from geometry optimization
does not hurt, I will apply RESP method to more than 200 conformations of
my other ligands.
I appreciate your and Francisco's recommendation of RESP in advance.
Sincerely,
Crystal
On Wed, Nov 23, 2011 at 5:05 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Nov 22, 2011, Crystal.CHIA-YU Ku wrote:
> >
> > I am looking for suggestions to solve the problem of installation of
> mopac
> > of Amber.
>
> We no longer provide mopac as a part of Amber. Googling on "mopac" will
> help
> if you want to compile the program yourself.
>
> [FWIW: I continue to recommend R.E.D. for this problem.]
>
> ...good luck....dac
>
>
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>
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Received on Wed Nov 23 2011 - 15:00:04 PST
