Re: [AMBER] How do I use for namd .dcd file?

From: sudipta <>
Date: Mon, 14 Oct 2013 06:08:01 -0700

I found there is some problem with ligand. The ligand senses extra three
atoms from the .prmtop file which is quite strange. when I used the
strip_mask as
 strip_mask=":WAT:SOD:GC1" in file and consider complex as the
receptor (instead of using receptor-ligand complex) then the job
successfully finished.
the corresponding command line for that was

time mpirun -np 2 /home/sudipta/AMBER/amber12/bin/ -O -i -o FINAL_RESULTS_MMPBSA_NMODE.dat -sp
3jzb_complex_solv.prmtop -cp 3jzb_protein.prmtop -y
3jzb_protein_ligand_system_36.mdcrd > progress_mmpbsa.log

In the following step, I used ligand_mask and receptor_mask in the


The command line that used is given below

time mpirun -np 2 /home/sudipta/AMBER/amber12/bin/ -O -i -o FINAL_RESULTS_MMPBSA_NMODE.dat -sp
3jzb_complex_solv.prmtop -cp 3jzb_complex.prmtop -rp 3jzb_protein.prmtop
-lp 3jzb_ligand.prmtop -y 3jzb_protein_ligand_system_36.mdcrd >

is the above syntax correct?

On Sat, Oct 12, 2013 at 5:06 PM, Jason Swails <>wrote:

> On Sat, Oct 12, 2013 at 1:31 PM, sudipta <> wrote:
> > Hi Jason,
> >
> > another problem which I am facing during mmpbsa calculation. it is
> showing
> > that the number of atoms in .prmtop file mismatches with the no of atoms
> in
> > .inpcrd file which is generated by program.
> >
> > FATAL: NATOM mismatch in coord and topology files
> >
> > However, I am not clear about this. Please give some suggestions
> regarding
> > this.
> >
> Find out if it is happening with your complex, receptor, or ligand topology
> files and try to figure out why this mismatch is occurring.
> Common mistakes include creating incompatible topology files to start with,
> specifying an incorrect receptor_mask and/or ligand_mask (although using
> the default masks helps in this case), and having some ions or water
> molecules in your complex system that are stripped out by the default value
> of strip_mask.
> It helps to understand the workflow that does behind the scenes,
> as it helps when trying to debug these types of problems.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Oct 14 2013 - 06:30:02 PDT
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