Re: solvating protein

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Dec 26 2008 - 19:53:29 CST

Hi Jorgen,
two things...

Jorgen Simonsen wrote:
> ridigbond water
>
> wrapAll on
> wrapWater on
Is this precisely what is in your config file? The proper command is
rigidbonds; this should crash namd.

Also, do the "strange" water configurations occur immediately or after
some amount of minimization? Are they present in the starting structure?

Best,
Peter
>
> 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
>
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:19 CST