Re: [AMBER] Periodic Box Size and Charge Determination

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 22 Jul 2015 09:06:10 -0400

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 - 06:30:03 PDT
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