Re: [AMBER] No solvent overlap

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 9 Jul 2010 10:58:36 -0400

which leap are you using? sleap or tleap? I'm pretty sure that sleap
required a bugfix, but that type of script worked just fine for me when I
used sleap. It may also help if you can send some pictures showing us what
you're talking about.

Good luck!
Jason

On Fri, Jul 9, 2010 at 10:13 AM, Thomas Exner
<thomas.exner.uni-konstanz.de>wrote:

> Dear amber users,
>
> I am trying to simulate a protein-DNA complex. But I have some problems
> to set up a water box with physiological salt concentration. Some of the
> ions are placed outside of the box during the grid calculation. In a
> periodic boundary simulation, these ions would lie in another box and
> probably overlap there with some water molecules or even the solute of
> this box. What is going wrong here and how can I fix this? The strange
> thing is that the same input worked pretty fine with amber8. Here is the
> input for leap:
>
> source leaprc.ff99bsc0
> loadoff DCP_final.lib
> loadoff MG.off
> TAQ = loadpdb 3ktq.pdb
> mods = loadAmberParams frcmod_phosphate
> solvateoct TAQ TIP3PBOX 12
> addions TAQ Na+ 66 Cl- 44
> saveamberparm TAQ taq.top taq.xyz
> quit
>
> Any help would be highly appreciated.
>
> Cheers,
> Thomas
>
> --
>
> ________________________________________________________________________________
>
> Dr. Thomas E. Exner
> Juniorprofessur "Theoretische Chemische Dynamik"
> Fachbereich Chemie
> Universitšt Konstanz
> 78457 Konstanz
>
> Tel.: +49-(0)7531-882015
> Fax: +49-(0)7531-883587
> Email: thomas.exner.uni-konstanz.de
>
> ________________________________________________________________________________
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 09 2010 - 08:00:07 PDT
Custom Search