Re: solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sun Mar 02 2008 - 23:53:14 CST

On Sun, Mar 2, 2008 at 10:56 PM, Steven Samuel Plotkin
<steve_at_physics.ubc.ca> wrote:
>
>
> Dear NAMD users,

Dear Steven,

>
> I am having a strange problem that I can't seem to track the source of.
>
> If I solvate the files ubq.pdb and ubq.psf ( for files see url links
> http://www.physics.ubc.ca/~steve/NAMD/ubq.pdb and
> http://www.physics.ubc.ca/~steve/NAMD/ubq.psf)
>
> with the following command in VMD:
> % solvate ubq.psf ubq.pdb -t 6 -o 5test_wb_ubq
>
> I get a nice water box around it, with 6 Angstrom distance from box
> boundary to protein.

This is okay, as expected.

>
> If I solvate the files 5test_sod.psf and 5test_sod.pdb
> (for files see url links
> http://www.physics.ubc.ca/~steve/NAMD/5test_sod.pdb and
> http://www.physics.ubc.ca/~steve/NAMD/5test_sod.psf)
>
> with the command:
> % solvate 5test_sod.psf 5test_sod.pdb -t 6 -o 5test_wb_sod
>

The problem is simple. If you take a look at the original structure,
there is a "floating" atom 128 A away from the protein (it seems that
is a SG from an Alanine, which is completely wrong!). That's why
you're getting this huge box of water. I'd suggest you to check the
structure or use a better template (there are tons of small proteins
that you can use as a test cases).

Good luck!
Michel

> I get a gigantic water box surrounding the protein. Looking at the output
> it seems to have replicated the box 2X2X2 for reasons that are unclear to
> me.
>
> The output of the ubq solvation is gives 8053 atoms after solvation. The
> output of the 5test_sod solvation gives 99265 atoms after solvation- way too
> much. The distances of the waters are up to 100 Anstroms away.
>
> The solvation of 5test_sod does not stop after the first segment like it
> should. Instead it seems to keep replicating segments 8 times, apparently
> replicating the unit cell to make a 2x2x2. I don't want it to do this, this
> takes up enough memory my RAM overflows on my workstation and I get a seg
> fault. I want a 1x1x1.
>
> I can't understand what is different about the psf and pdb files that is
> making the solvate command do this?
> I thought it might have been a metal atom inside the protein, but I removed
> it and still the problem remains.
>
> links to the output of my solvate commands are here:
> http://www.physics.ubc.ca/~steve/NAMD/output_solvate_ubq.txt
> http://www.physics.ubc.ca/~steve/NAMD/output_solvate_sod.txt
>
> links to the pdb and psf files are above in case that helps.
>
> Sorry if this is a basic question or if the answer is obvious, any help is
> greatly appreciated.
>
> Steve P.
>
>
>

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