On Mon, Apr 11, 2016 at 10:11 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
> Dear experts,
>
> I am in my final stage of a part of my research and I have already ran
> simulation without any problem. I also ran PBSA and GBSA calculation
> without any issues. Now what I want to do to wrap up this part of research
> is to perform alanine mutagenesis for some residues (one at a time) to
> compare with experimental data. I followed the ras-raf tutorial and
> successfully ran the alanine scanning mutagenesis. But when I try to follow
> exact same procedure in my system, I get following errors everytime:
>
>
> Input file:
>
> &general
>
> startframe=500, endframe=3500, interval=5,
>
> verbose=2, keep_files=2, strip_mask=':WAT,CL',
>
> /
>
> &gb
>
> igb=5, saltcon=0.150,
>
> /
>
> &pb
>
> inp=1, radiopt=0, istrng=0.15, fillratio=4.0
>
> /
>
> &alanine_scanning
>
> /
>
> Loading and checking parameter files for compatibility...
> File "/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/MMPBSA.py",
> line 102, in <module>
> app.loadcheck_prmtops()
> File
>
> "/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 586, in loadcheck_prmtops
> FILES.mutant_ligand_prmtop)
> File
>
> "/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
> line 109, in __init__
> self._validate()
> File
>
> "/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
> line 876, in _validate
> raise PrmtopError('Complex natom != receptor natom + ligand natom')
> PrmtopError: Complex natom != receptor natom + ligand natom
> Exiting. All files have been retained.
>
The important thing here is that the 3 mutant prmtops need to be
consistent, as does the 3 wild-type prmtops. So when doing alanine
scanning, you will need exactly 2 "additional" prmtops. You will need a
mutated complex and either a mutated receptor *or* a mutated ligand. And
the mutant complex must have the same number of atoms as the mutant
receptor + regular ligand (if the mutation is in the receptor) or mutant
ligand + regular receptor (if the mutation is in the ligand).
This is not true in your files, so you have to figure out why. You can
check this easily yourself by just looking at the top of each of your
prmtops. The first number in the POINTERS block is the number of atoms in
your system. Do the addition by hand and see what you get. If they *are*
consistent, double-check your command-line flags.
HTH,
Jason
--
Jason M. Swails
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Received on Wed Apr 13 2016 - 10:00:06 PDT
