Re: [AMBER] Periodic Box Size and Charge Determination

From: Jason Swails <>
Date: Wed, 22 Jul 2015 09:06:10 -0400

On Wed, Jul 22, 2015 at 8:43 AM, Aronica, Pietro <> wrote:

> Thank you for your reply.
> Because of my workflow, I find myself needing to input fully solvated pdbs
> (with octahedral boxes) back into LEaP for further simulations and
> modifications. This step involves manually setting the box with the "set
> PDB box NUM" command (and changing the angles in the prmtop and inpcrd from
> square to octahedral). Up to now, I've taken NUM from the restart file I
> created the pdb from, but this was clunky and always required me to check
> the restart file. If you tell me there is no way to calculate the box size
> from the pdb, I will go back to it, but I thought it would be a relatively
> simple coordinate calculation to output the correct value.
> As for the charge calculation, I know pdbs have no charge, but they do
> have the number of ASP, GLU, LYS and ARG, as well as counterions, so I
> thought it would be trivial to sum accordingly and give the overall charge.
> If there is no existing program, I guess I'll just write my own.

‚ÄčIn PDB files, ASP is used to represent *all* protomers, so if you get an
NMR-resolved structure with a carboxylate hydrogen from the PDB, its charge
will be neutral, but its name will still be ASP. This is more of an issue
for HIS, which can be +1 or neutral at pHs very close to 7.

As an aside, newer versions of cpptraj *should* write PDB files with CRYST1
records when generating a PDB from a system that has unit cell dimensions
defined. So maybe this will help your workflow (since the periodic box
will be defined directly in the PDB file).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jul 22 2015 - 06:30:03 PDT
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