Re: [AMBER] Antechamber

From: Jasim, Mahmood (Student) <"Jasim,>
Date: Tue, 17 Sep 2013 10:58:56 +0000

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 [] 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

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Received on Tue Sep 17 2013 - 04:00:03 PDT
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