AMBER: Extracting Coords&MMPBSA&ambpdb

From: Srinivas Odde <>
Date: Tue, 24 Apr 2007 10:51:48 -0500

Dear Amber users,
I have extracted the coordinates from the trajectories as we discussed
earlier. After the extraction process as you suggested I thought of
converting the second coordinates ( to pdb by using
the ambpdb option.
When I look into those converted pdb structure, my ligand is completely
screwed up there and some bonds are missing
I have checked the trajectory by loading into VMD it is fine and no
problem with the ligand during the 3ns simulation

I have also converted my prod.rst file to pdb with the same ambpdb and
looks alright.
I don't know whether extracting process or ambpdb screwed up ligand
coordinates and bonds.

Due to this problem I am unable to run binding energy calculations for
this case. If any one has idea how to resolve it, kindly write me back.



-----Original Message-----
From: [] On Behalf
Of David A. Case
Sent: Monday, April 23, 2007 4:17 PM
Subject: Re: AMBER: Problems with AMBER8 on 32-bit FC6

On Mon, Apr 23, 2007, David LeBard wrote:
> I am having troubles compiling a serial version of AMBER8 on a 64-bit
> Pentium D running a 32-bit version of Fedora Core 6.

I think generally there are three options:

1. add "-m32" to the CFLAGS option in config.h, and recompile LEaP

2. just use tleap (not xleap), since it is 64-bit clean (I think)

3. upgrade to Amber 9, where problems like this seem to go away.

....hope this helps...dac
...hope this helps...dac

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Received on Wed Apr 25 2007 - 06:07:33 PDT
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