Re: [AMBER] Antechamber

From: Jasim, Mahmood (Student) <"Jasim,>
Date: Mon, 16 Sep 2013 11:12:23 +0000

Regarding -ek flag I tried adding -ek"PM3" and -ek"MOPAC" to the command for the prepi file and both did not waork, I did not get any new files.
From: David A Case []
Sent: 13 September 2013 17:17
To: AMBER Mailing List
Subject: Re: [AMBER] Antechamber

On Fri, Sep 13, 2013, Jasim, Mahmood (Student) wrote:

> Thank you so much for your reply. I do run the procedure as you said
> and load the ligand files into leap followd by the complex. I finally
> solvate the model and save the prmtop and inpcrd files. I convert the
> inpcrd file into a pdb file to view it and here I find that the ligand
> position within the protein has changed from the starting conformation.

The above description to too qualitative. You are telling us what you
intended to do, not what you really did (i.e. not the exact commands you
used.) LEaP does not change relative coordinates from the initial pdb file.
Make sure you are loading a single pdb file, with correct coordinates for
both the protein and the ligand.

> Can I also ask about the -ek falg, where does it go within the command
> and how I specify PM3?

What did you try and what was the result? (If the manual is unclear,
experimentation is often very helpful.) It is probably most intuitive to
edit the file.


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