Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb

From: <sunita.tifrh.res.in>
Date: Wed, 10 Sep 2014 18:51:50 +0530

Thank you guys. I got my answer.

I find the mismatch after seeing it in VMD. When I was trying to see the
added ion for the same resid it was showing two molecules. Then I got
confused. Now the understanding is clear.

Thanks and regards,
Sunita

> On Wed, Sep 10, 2014 at 5:14 AM, <sunita.tifrh.res.in> wrote:
>
>> Looks like the problem exists when the number of water molecules exceed
>> more than 9999. Please try to find out why is so?
>>
>
> €‹You've already heard the explanation about why this is so. I'll chime
> in
> with my 2c and say that ambpdb gives the _desirable_ behavior, in my
> opinion. Most programs that I've seen are fairly strict when it comes to
> expecting certain items to occupy certain columns in PDB files (they may
> be
> less strict about requiring that all 'mandatory' fields be populated).
> When residue numbers go above 9999, the coordinates will be shifted by 1
> character and could yield very strange visualization artifacts.
>
> For instance, if you try viewing the PDB files with VMD, only the one
> printed by ambpdb will actually render correctly for precisely this
> reason.
> In fact, if you use VMD to print out PDB files with atom and residue
> numbers that overflow their fields, you may be even more surprised than by
> what ambpdb does ;). VMD switches to a hexadecimal integer representation
> once numbers no longer fit into their fields. So the residue numbers
> would
> go from 9999 to 2710 and atom numbers would go from 99999 to 186a0 :).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
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>



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Received on Wed Sep 10 2014 - 06:30:02 PDT
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