[AMBER] No solvent overlap

From: Thomas Exner <thomas.exner.uni-konstanz.de>
Date: Fri, 09 Jul 2010 16:13:31 +0200

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
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Received on Fri Jul 09 2010 - 07:30:03 PDT
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