solvating protein

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Fri Dec 26 2008 - 10:27:31 CST

Hi all,

I have a protein that I want to solvate but I get into problems when I try
to minimize the complex freezing the protein. I give me some strange
configurations of the water molecules and I am not quite sure how to resolve
this problem. I have look into my psf-files; for the protein structure
itself I don't get any problem generating the psf-file then I try to solvate
it

package require solvate
solvate protein.psf protein.pdb -t 12 -o wb_protein

the psf files generates the protein segments without angles

 REMARKS segment P1 { first NTER; last CTER; auto none dihedrals }
 REMARKS segment O1 { first NONE; last NONE; auto none dihedrals }
 REMARKS segment W1 { first NONE; last NONE; auto none dihedrals }

but here I don't quite understand why it generates a dihedrals for some of
the crystal water (segment O1 and W1 in this case)

but it should include the angles as well I presume for the water it seems
okay

 REMARKS segment WT1 { first NONE; last NONE; auto none }
 REMARKS segment WT2 { first NONE; last NONE; auto none }
 REMARKS segment WT3 { first NONE; last NONE; auto none }
 REMARKS segment WT4 { first NONE; last NONE; auto none }
 REMARKS segment WT5 { first NONE; last NONE; auto none }

For the NAMD configuration file I am using the option:

ridigbond water

wrapAll on
wrapWater on

but still gives these strange water structures where the hydrogens are near
the protein and the oxygen is 95 away....

Any help to get me out of this - thanks in advance

Best regards

Jorgen

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