Could you email what are the masks for complex, protein and ligands?
And, you can always check the number of atoms in prmtop by using cpptraj.
$ cpptraj -p prmtop_file_name
>> parminfo
Output --
*Topology prmtop contains 34622 atoms.*
Title: default_name
10661 residues.
10453 molecules.
34652 bonds (32947 to H, 1705 other).
6005 angles (3684 with H, 2321 other).
14711 dihedrals (7467 with H, 7244 other).
Box: Trunc. Oct.
10441 solvent molecules.
Final solute residue is 220
GB radii set: modified Bondi radii (mbondi)
parminfo command will let you know the number of atoms in any prmtop. Then
you can simply sum the number of atoms in protein and ligand prmtop files
to find out which one has the wrong number of atoms.
Pancham
On Wed, Apr 25, 2018 at 3:00 PM, Núbia Prates <nnubiaits.hotmail.com> wrote:
> >Do you have the same problem without asking for alanine scanning?
>
> No, I don't.
>
>
> > Is the above the entire error message?
>
> This is the entire error message :
>
> File "/home/amber16/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.
>
>
> Is it possible, instead of following the alanine scanning tutorial, to
> calculate the free energy of a mutate protein-protein complex just as the
> tutorial for a non-mutated complex?
>
>
> ________________________________
> De: David A Case <david.case.rutgers.edu>
> Enviado: terça-feira, 24 de abril de 2018 22:15
> Para: AMBER Mailing List
> Assunto: Re: [AMBER] Issue running alanine scanning
>
> On Tue, Apr 24, 2018, Núbia Prates wrote:
> >
> > I am trying to run an alanine scanning calculation on the binding free
> > energy of protein-protein complexes.
> >
> > PrmtopError: Complex natom != receptor natom + ligand natom*
> >
> > I verified the prmtop file of the complex, and it have the same atom
> > numbers as the sum between receptor.prmtop and ligand.prmtop atoms.
>
> Do you have the same problem without asking for alanine scanning? Is
> the above the entire error message? You may have to modify whatever
> scripts you are using to print the three natom numbers it is complaining
> about, which may help in tracing down the problem.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
> lists.ambermd.org
> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related software to ask questions related to AMBER and Molecular
> Dynamics Simulations in general.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 26 2018 - 09:00:02 PDT
