AMBER Archive (2008)

Subject: Re: AMBER: MM-PBSA/NMODE in Amber 10

From: Daniel Oehme (oehmes4_at_gmail.com)
Date: Mon Sep 15 2008 - 20:23:26 CDT

Matt,

I have just recently tried to do some NMODE calculations using MM-PBSA
in AMBER 10 and had the same issue. My work around was to edit line 96
of mm_pbsa_createinput.pm to 'print OUT " ntxo = 1,\n";' instead of
'print OUT " ntxo = 0,\n";' Sander no longer allows output of an
unformatted restart file so ntxo has to be set to 1 in the nmode input
file.

Daniel Oehme
PhD student
La Trobe University

On Tue, Sep 16, 2008 at 6:37 AM, Peterson, Matthew W. (MPETERSON)
<mpeterson_at_mitre.org> wrote:
> Iım having some trouble getting normal mode calculations to work using the
> mm_pbsa.pl script in AMBER 10.
>
> I tried running the example, and I got this:
>
> =>> Calculating energy / entropy contributions
> Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_lig.crd.1
> Minimize structure
> /projects/BIO/sw/amber10/exe/sander -O -i sanmin_lig.in -o
> sanmin_lig.1.out -c ../01_GenerateSnapshots/ras_raf_II_wt_lig.crd.1 -p
> ../raf_wt.prmtop -r sanmin_lig.1.restrt not running properly
>
> If I look at sanmin_lig.1.out, I find the following error:
>
> NTXO ( 0) must be 1.
>
> (ntx0=0 is no longer supported)
>
> I also was having some trouble with the binding scripts, until I followed
> the solution posted here
> (http://amber.ch.ic.ac.uk/archive/200806/0088.html).
>
> Has anyone had any luck running these scripts "out of the box?" I'm trying
> to figure out if this is a configuration error on my part, or issues with
> the mm_pbsa.pl scripts and modules.
>
> Thanks,
>
> Matt
>
> Matthew Peterson
> The MITRE Corporation
> mpeterson_at_mitre.org
>
>
>
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