AMBER Archive (2004)

Subject: RE: AMBER: add Na+

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Tue Feb 24 2004 - 13:29:36 CST

Thank you for reply. Now I have got 3 visible Na+. But when I ran antechamber
with this command :

 antechamber -i DNa3.pdb -fi pdb -o DNa3.prep -fo prepi -c bcc -nc -1 -at amber

It complained :

when using :

  antechamber -i DNa3.pdb -fi pdb -o DNa3.prep -fo prepi -c gas -nc -1 -at amber

I got the output file :

......................................
  48 H49 H1 E 47 43 41 1.089 109.736 164.838 0.094
  49 O41 OS M 47 43 41 1.410 109.647 -74.908 -0.346
  50 S42 SO M 49 47 43 1.619 120.495 -55.590 1.214
  51 O43 O E 50 49 47 1.440 108.234 -54.758 -0.345
  52 O44 O E 50 49 47 1.441 108.259 173.917 -0.345
  53 O45 O M 50 49 47 1.610 102.709 59.556 -0.345
  54 X 1 0 1 0.553 nan 63.375 0.000
  55 X 1 0 1 0.553 nan 63.375 0.000
  56 X 1 0 1 0.553 nan 63.375 0.00

Do you have any suggestion about this? Thank you very much.

Lan
 

Quoting Ross Walker <ross_at_rosswalker.co.uk>:

>
> > I want to add 3 Na+ to my molecule. I found that there is Na
> > ion in ion94.lib.
> > But it seems that it is invisible. I am curious why it is
> > like this. How can I
> > make it visible when I add 3 Na+ to my molecule? Thanks in advance.
>
> Open your molecule in xleap:
>
> model = loadpdb myfile.pdb
>
> and then run the command:
>
> addions model Na+ 3
>
> This will create a 1 angstrom resolution charge grid around your molecule
> and add 3 Na+ ions at the three points of highest negative potential.
>
> For more info refer to the xleap manual or the DNA tutorial on the amber
> website http://amber.scripps.edu/tutorial/polyA-polyT/index.html
>
> All the best
> Ross
>
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