(no subject)

From: noor gaffoor <nisha_noor_at_yahoo.com>
Date: Sun 11 Feb 2001 21:08:17 -0800 (PST)

Dear Sir,

I am doing my molecular dynamics with Amber for my dna
system. I want to do the calculations in 1M NaCl as
well as in 1M Na+ solutions. I like to verify the
methodology that I have followed for the preparation
of the above solutions.
The following commands I used in tleap.
  1) > parm94 = loadamberparams parm94.dat

  2) > saveoff parm94 parm94.lib

  3) > temp= loadpdb amber6.pdb

  4) > addions tem Na+ 0

  5) > solvatebox temp WATBOX216 9 1

  Here I got the box dimension as,

    a= 48.9085,b=49.2854,c=77.68475, and I have
calculated that, 56 Na 56 Cl ions are needed to
achieve 1M sodium chloride solution and 112 Na to
reach 1M Na solution.
Then I used the following commands to get 1M Nacl
6) > addions temp Na+ 52

7) > addions temp Cl- 52

8) > saveamberparm temp prmtop prmcrd

9) > quit

Also I like to know that whether I have used the
number of Na and Cl ions properly.
Please clarify my doubts.


Do You Yahoo!?
Get personalized email addresses from Yahoo! Mail - only $35
a year! http://www.rosswalker.co.uk/adsense_opt/
Received on Sun Feb 11 2001 - 21:08:17 PST
Custom Search