Re: [AMBER] Parameters for ATP and MG2+

From: Jason Swails <>
Date: Wed, 13 Aug 2014 12:24:23 -0400

On Wed, 2014-08-13 at 14:56 +0000, Valentina Romano wrote:
> Dear Amber users,
> I used tleap to parametrize a complex og a kinase bound to ATP and 2 MG2+ ions.
> I used the following input file:
> source leaprc.ff99SB
> loadamberparams ATPphos.frcmod
> loadamberprep ATP.prep
> COMPLEX = loadpdb PknGATP_init_min_vac.pdb
> alignAxes COMPLEX
> addions COMPLEX Na+ 6
> solvatebox COMPLEX TIP3PBOX 8.0
> saveamberparm COMPLEX PknGATP_wt.prmtop PknGATP_wt.inpcrd
> quit
> The log file contained the following messages:
> Loading parameters: ./ATPphos.frcmod
> Loading Prep file: ./ATP.prep
> Loading PDB file: ./PknGATP_init_min_vac.pdb
> One sided connection. Residue: MG2 missing connect0 atom.
> etc...
> What does the last sentence mean?
> Was the Mg2+ well parametrized or not ?

For some reason it was trying to connect MG2 to the previous residue
possibly because the definition of the previous residue is a mid-chain
residue with a defined tail atom. What happens if you add a TER card
before the MG2 atom? Does this warning go away? Do you see a hanging
valence from the resulting prmtop and incprd files when you view them
with VMD?

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Aug 13 2014 - 09:30:03 PDT
Custom Search