Re: [AMBER] Antechamber

From: Jasim, Mahmood (Student) <"Jasim,>
Date: Mon, 16 Sep 2013 09:34:50 +0000

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. I also noticed some destruction in the ligand itself but this disappears after I perfomed the minimization, however the position of the ligand is still different from the starting conformation. The commands I used are as follows (the ligand file is LIG.pdb and the complex is complex.pdb):

nohup $AMBERHOME/exe/antechamber -i LIG.pdb -fi pdb -o LIG.prepin -fo prepi -c bcc -s 2 &

$AMBERHOME/exe/parmchk -i LIG.prepin -f prepi -o LIG.frcmod

$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB

source leaprc.gaff

loadamberprep LIG.prepin

loadamberparams LIG.frcmod

model=loadpdb complex.pdb

addions model Na+ 0

solvateoct model TIP3PBOX 8.0

saveamberparm model wat.prmtop wat.inpcrd

$AMBERHOME/exe/ambpdb -p wat.prmtop < wat.inpcrd > wat_inpcrd.pdb

These are the commands I am using. Also how can I edit the file as I cannot see it until the prepi file is generated and not before.

Mahmood Jasim

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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Received on Mon Sep 16 2013 - 03:00:03 PDT
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