Hello Jason,
My input file is as follow. I did not have many changes to the default parameters. My system is a DNA segment solvated in an truncated octahedron box. I have tried to supply the unsolvated prmtop created by myself from cpptraj and one created using the ante-MMPBSA.py script. I have also tried running MMPBSA.py by giving it only the unsolvated prmtop. The stripped mdcrd while for this was created with trajout in cpptraj. In all cases, the same problem occurred.
&general
keep_files=0, entropy=1,
/
&gb
igb=1, saltcon=0.400,
/
My command for running it is
MMPBSA.py -O -i dna.in -o -dna-mmpbsa.txt -sp dna-solvated.prmtop -cp dna-stripped.prmtop -y dna-solvated.mdcrd or
MMPBSA.py -O -i dna.in -o -dna-mmpbsa.txt -cp dna-stripped.prmtop -y dna-stripped.mdcrd
Thanks.
Huy Le
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, May 06, 2013 9:51 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA.py error
Can you send me your input files? I've never seen this before...
Thanks!
Jason
On Mon, May 6, 2013 at 9:39 AM, Le,Huy Tuan <huy.le.louisville.edu<mailto:huy.le.louisville.edu>> wrote:
> Hello,
>
> My MMPBSA.py calculations error out whenever I try entropy=1
>
> I notice the error in the ptraj input file attached below which list
> the residue as ",0-25" instead of ":1-25" When I make this change
> manually using the -make-mdins and use-mdins flags there's no error.
> Has anyone else ran into this problem before and if so how do you fix it?
>
> _MMPBSA_ptrajentropy.in
> trajin _MMPBSA_complex.mdcrd
> reference _MMPBSA_avgcomplex.pdb
> rms mass reference ,0-25
> matrix mwcovar name comp.matrix ,0-25
> analyze matrix comp.matrix out _MMPBSA_complex_entropy.out thermo
> reduce
>
> Thanks
>
> Huy Le
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon May 06 2013 - 07:30:03 PDT
