On Sat, Oct 01, 2011, Giulia Palermo wrote:
>
> I am working with a very big DNA/protein complex (170000) atoms and I am
> using the ff99SBildn force field.
>
> When I try to build the topology and coordinate files (either with tleap
> or sleap) everything seems ok.
> The problem is that the two tools do not consider all the water molecules.
> So, in the final .pdb file, I have less water molecules with respect to
> the original starting point.
Your description is not detailed enough to be helpful. Can you say exactly
what commands you gave, what you mean by "the two tools", "the starting
point", etc. (Is the problem that there are water molecules in the "original"
pdb file that are not in the final result? If so, please check how the waters
are identified in the intial pdb file.) But I'm really guessing: we need to
know exactly what you did and what the problem is.
....dac
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Received on Sun Oct 02 2011 - 10:30:04 PDT
