Re: Problem facing during Solvation of Coarse Grain Model

From: Peter Freddolino (
Date: Tue Sep 14 2010 - 18:59:54 CDT

Hi Sunita,

On 09/14/2010 04:04 AM, sunita gupta wrote:
> 1. The water box I am getting after using the command *- solvate
> cg_protein_membrane.psf cg_protein_membrane.pdb -o solvate -b 4.0 -z
> 12.0 +z 12.0 -spsb cgwat.pdb -spsf cgwat.psf -stop -ws
> 40 -ks {name WAT} *is having an extra patch at one side. along with
> this error message* "*-error Found 2419 water atoms near the solute!
> Please report this bug to -error
> <>, including, if possible, your psf and pdb
> file.*"* Find the attachment 1 showing extra patch.
Could you provide the psf and pdb, as requested in the error message?

By the way, the "extra patch" is probably not actually an extra patch.
Try looking at it in orthographic (rather than perspective) mode, and I
bet you'll see that it is being caused by the one random lipid jutting
out into space there. You may instead need to specify the water box
dimensions explicitly to prevent excess water from being added to cover
the entire molecule.

> 2. In order to get over with this error I tried another protocol ie.
> Solvate the entire all-atom (protein and lipid) with standard water
> molecule by - *solvate protein_membrane.pdb protein_membrane.psf -o
> solvate_allatom -b 1.5 -z 15.0 +z 15.0 *and then converted the whole
> system to CG representation It seems to b fine without any extra patch
> (Find as attachment 2)
> kindly guide me which of the above protocol is correct? and how to
> deal with the error occuring in protocol 1.
It is much better with this model to add solvent after coarse graining.
Otherwise one can end up with some very unusual water positions because
water beads are placed at the centers of mass of the corresponding
clusters of atoms, which are unlikely to be co-located in space.

> Thanks in Advance
> --

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