This should be accomplishable using leap
[x/t]leap
source leaprc.[APPROPRIATE TYPE].[APPROPRIATE FF]
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 <aashivku.ucsd.edu> 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
> UCSD
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Received on Thu Nov 05 2020 - 03:30:02 PST
