> 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.
This should work fine and works for me (although putting a long
straight DNA into a linear box is likely not what you want unless you
want to represent an aggregated fiber since the periodic images will
likely interact)...
I have noted with certain compiler combinations (pgf90 on Linux) that the
solvate commands in LEaP do not perform correctly and create a partial
slab near the solute with significantly less water than is required to
solvate. I have yet to track the cause and work around this by using LEaP
compiled by a different compiler or OS. Try using amber on another system
or send me the PDB file and I can attempt to reproduce the problems.
[Regarding the ambpdb issue, the PDB format only supports residue numbers
3 letters in length and atom numbers so for large systems, there is
overflow until we introduce "chains" or wrap the numbers back to zero. I
think you/we should be able to get LEaP to work correctly as I've built
nucleic acid systems this large or larger...]
\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
|
| tec3.utah.edu (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418
http://www.chpc.utah.edu/~cheatham
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Received on Wed Apr 20 2005 - 15:53:00 PDT
