AMBER Archive (2004)

Subject: Re: AMBER: add Na+

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 24 2004 - 13:35:06 CST

On Tue, Feb 24, 2004, L Jin wrote:

> 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

Antechamber is for _organic_ molecules; it doesn't know about sodium ions.
Furthermore, antehcamber is designed to look at one (relatively) small
molecule at a time; you cannot give it multiple molecules.

...hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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