Jason,
Thanks for your reply.
I checked the number of atoms for my system and it is as follows:
Mutant_complex: 3930
Mutant_A : 3021
B: 909
For wild type:
Wild_complex: 3944
A : 3035
B: 909
There is difference in atom numbers between prmtop from wild type Vs Mutant
for complex and protein A but isn't the change in atom number expected as
we are deleting extra atoms to mutate to alanine? The wildtype nA + nB =
number of atoms in the wildtype complex. Same for mutant as well. But the
error is saying that it is not the case.
I also tried to manually change the atom number in mutant to match the atom
number of the wild type but got different error message. Any thoughts on
this would be helpful.
Also, you mentioned about changing the flags in the command line in the
previous email. Do you mind explaining that a little bit more? All the
receptor and ligand protein are already specified. So I was wondering what
else we could change/check for flags?
Thanks again,
Sincerely,
Jag
On Wed, Apr 13, 2016 at 12:53 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Apr 13 2016 - 15:30:03 PDT
