[Chimera-users] Problem with added ions in Amber

George Tzotzos gtzotzos at me.com
Tue Aug 8 11:37:26 PDT 2017


In MD movie I loaded complex.prmtop and complex.inpcrd files

In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I’m attaching a snapshot showing the Na+ ions in red).

I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 
NOTE: I unticked the Removed existing ions/solvent box

I obtained the following Warning “Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA

I generated complex_solv.prmtop and complex_solv.inpcrd files

When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below).
> resinfo
#Res  Name First  Last Natom #Orig  #Mol
    1 ASP      1    14    14     1     1  
    2 THR     15    28    14     2     1  
———————
  250 LEU   3988  4006    19   250     3  
  251 VAL   4007  4023    17   251     3  
  252 KBR   4024  4062    39   252     4  
  253 WAT   4063  4065     3   253     5  
————
10272 WAT  34084 34086     3 10272 10024  
10273 WAT  34087 34089     3 10273 10025 


Is this what should be expected? Should I consider the solvated complex charge neutralised?

Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions 

Thank you in advance for any suggestions.

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