Re: [AMBER] Saving pdb as parm7/prmtop file with boundary conditions

From: Gustaf Olsson <>
Date: Thu, 5 Nov 2020 11:17:09 +0000

This should be accomplishable using leap

    sys = loadPdb [PDB-FILENAME]
    check sys
    setbox sys vdw
    saveamberparm sys [PRMTOP] [INPCRD]

I don’t know what is in your PDB file so you need to select the appropriate parameters to source, water, lipid, protein…

If there are no deviations/problems, the suggested commands should “box” input files for your simulation. The PBC and other details are then defined in the input files.

// Gustaf

> On 5 Nov 2020, at 09:11, Aashish Shivkumar <> wrote:
> Hi,
> I got my amber input pdb from charmm-gui. How do I save it as a
> parm7/prmtop file with the periodic boundary conditions and the box size?
> Thanks!
> -Aashish Shivkumar
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Received on Thu Nov 05 2020 - 03:30:02 PST
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