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

From: Jason Swails <>
Date: Mon, 14 Oct 2013 09:16:30 -0400

On Mon, Oct 14, 2013 at 9:08 AM, sudipta <> wrote:

> 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
> 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
> mmpbaa.infile.
> strip_mask=":WAT:SOD",
> receptor_mask=:1-4197,
> ligand_mask=:4198-4244,
> The command line that used is given below
> time mpirun -np 2 /home/sudipta/AMBER/amber12/bin/ -O -i
> 3jzb_complex_solv.prmtop -cp 3jzb_complex.prmtop -rp 3jzb_protein.prmtop
> -lp 3jzb_ligand.prmtop -y 3jzb_protein_ligand_system_36.mdcrd >
> progress_mmpbsa.log
> is the above syntax correct?

I don't think your receptor_mask and ligand_mask are correct, unless your
system is absolutely enormous. The ":" character denotes residue numbers
(not atom numbers), so your masks suggest you have over 4200 residues
(which is a very large system, indeed).

In any case, the default mask assignments should be sufficient for your
system (it is only known to fail when your 'ligand' is composed of multiple
residues separated by residues of the receptor in the complex topology
file, and you will be given a straight-forward error message if this is the
case). I would always suggest using the default mask assignments when
possible to avoid hitting errors like this.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Oct 14 2013 - 06:30:04 PDT
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