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
solution.
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.
by,
nisha
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Received on Sun Feb 11 2001 - 21:08:17 PST
