Re: [AMBER] Periodic Box Size and Charge Determination

From: Aronica, Pietro <>
Date: Wed, 22 Jul 2015 15:02:23 +0000

Thank you for your response.
I do not expect to mess around with protonated HIS or neutral ASP, so, for now, I have just written a short script that sums up all charged amino acids and counterions and outputs the overall charge.
For cpptraj, how can I include CRYST1 records to pdbs? The manual is no help, and the only clues I find online are patchlogs saying that the feature is now implemented. Do I need to have prmtop and restart in a special format? The prmtop does have a FLAG BOX_DIMENSIONS, and the restart does have that last line indicating box size and angles. Is something else needed? I have cpptraj V15.00b, so it seems to me I have the latest version.
Short aside, I can't seem to apply update.1. I get the following error message:

PatchingError: .patches/AmberTools15_Unapplied_Patches/update.1 failed to apply. No changes made from this patch

Is that cause for concern?
Kind regards

-----Original Message-----
From: Jason Swails []
Sent: 22 July 2015 14:06
To: AMBER Mailing List
Subject: Re: [AMBER] Periodic Box Size and Charge Determination

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
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Received on Wed Jul 22 2015 - 08:30:05 PDT
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