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
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 13 2014 - 09:30:03 PDT
