Dear Sir
I have tried your suggestion and not solvate the system. The results were similar. I have attached the files for you to have a look please.
Regards
Mahmood Jasim
________________________________________
From: case [case.biomaps.rutgers.edu]
Sent: 16 September 2013 12:45
To: AMBER Mailing List
Subject: Re: [AMBER] Antechamber
On Mon, Sep 16, 2013, Jasim, Mahmood (Student) wrote:
> Sorry for my bad English. I did actually perform all the steps and
> manage to get the prmtop and inpcrd files. The problem is that when I
> convert the inpcrd file to a pdb file and view it in DS Visualizer,
> what I see is different from my starting complex conformation in terms
> of the position of the ligand.
What you did looks fine. I've never seen this sort of behavior. You might
see if the problem goes away if you don't solvate the system (just as a
debugging step.) You should probably try to find a minimal example that
shows the problem, and post the files that would be needed to reproduce it.
Basically, I can't think of any way in which the LEaP code would change the
relative orientation of protein and ligand from what was in the "complex.pdb"
file you started with.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/download attachment: LIG.pdb
Received on Tue Sep 17 2013 - 04:00:03 PDT
