On Fri, Apr 28, 2017, Miguel Rivera wrote:
>
> To start off: I built a membrane around a GPCR with a ligand already placed
> in it using CHARMMGUI and there force fields. I then took there outputs, in
> the amber format, and ran MD. Using the output pdb from what CHARMGUI gave
> me I then used an ante-mmpbsa.py script as follows:
>
> ante-MMPBSA.py -p step5_charmm2amber.parm7 -c complex.prmtop -r
> receptor.prmtop -l ligand.prmtop -n":279" -s":TIP3:MEMB:CLA:WAT:POPC"
>
> But it turns out that PDB is incorrect and it is actually 277 that is the
> ligand. So there may be something fishy here I am just not sure.
Amber renumbers residues when building systems. Use ambpdb to create an
"Amber" pdb file from your prmtop and restart files, and use that to look
at residue number.
> mpirun -np 20 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o test.dat -sp
> step5_charmm2amber.parm7 -cp complex.prmtop -rp receptor.prmtop -lp
> ligand.prmtop -y prod.nc -eo excel_out.csv
If you have problems, use MMPBSA.py (not MMPBSA.py.MPI) to simplify things,
using just a few snapthots. Look through the output files for errors.
>
> I receive an error saying there is something wrong with my complex.prmtop
> and the calculation failed.
> When I check the _MMPBSA_ files I read this error FATAL: NATOM
> mismatch in coord and topology files.
This is the important error message: the number of atoms in the complex.prmtop
file and the number of atoms in the complex trajectory don't match. Maybe
that will help you see what is wrong.
....dac
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Received on Sat Apr 29 2017 - 05:30:04 PDT
