Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber.

From: Miguel Rivera <>
Date: Thu, 4 May 2017 16:18:54 -0600

Hey thanks for the advice, I am looking into it but with no luck. I am
guessing that there are number inconsistencies in the .parm7 given from me
by charm gui server and the complex/ligand/receptor .prmtop files that I am
making. Do you know if there is an amber tool that can turn my parm7 file
to an "amber" prmtop file. Even though they are both parameters and are
both accepted. I am just trying to figure out what I can do to overcome

On Sat, Apr 29, 2017 at 6:28 AM, David Case <> wrote:

> 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 script as follows:
> >
> > -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/ -O -i -o test.dat
> -sp
> > step5_charmm2amber.parm7 -cp complex.prmtop -rp receptor.prmtop -lp
> > ligand.prmtop -y -eo excel_out.csv
> If you have problems, use (not 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 Thu May 04 2017 - 15:30:02 PDT
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