Dear all,
I want to run MD simulation for a DNA molecule, which is quite long in
its length (290 A). For this molecule, I added TIP3P water boxes using,
"solvatebox temp WATBOX216 9 1" (of tleap). When I visualised the
molecule using InsightII, I found that only one protion of the DNA
(ie. say right side) is fully covered with water and other portion of
the DNA is only 10% covered (total number of water molecule added to the
system is 22263), ie. 3/4th of the rectangular box in one of the sides of
DNA molecule remains vaccum. So, I tried the following commands:
solvateshell temp WATBOX216 9.0 1.0 and then solvatebox temp
WATBOX216 9 1 (total no. of water molecules is ~33000).
Now, I was unable to convert the prmcrd file into pdb format using
ambpdb although I have increased the dimensions of the parameters in
/src/etc/ambpdb.f file.
I wish to know, is there any limitation on adding the water
boxes; because I have been successfully using the same command
(solvatebox temp WATBOX216 9 1) for many DNA molecule with length of
about 85 A. I also wish to know whether the second method is correct
or not.
Will it possible for me to run the simulation for this DNA molecule
(+water+ions) using amber? Kindly, tell your suggestions.
Thank you very much in advance.
Sincerely,
thenmalar
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Received on Wed Apr 20 2005 - 09:53:00 PDT
