Re: [AMBER] Periodic Box Size and Charge Determination

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
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
Pietro

-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
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 < pietro.aronica07.imperial.ac.uk> 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).

HTH,
Jason

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 22 2015 - 08:30:05 PDT
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