Hello,
I'm now being very careful about the topology files generated by TLEAP
because the results I'm getting don't match some of those reported by
others.
When I change a leaprc file to reference the SPC water in solvents.lib
rather that TIP3P, by adding the following lines:
HOH = SPC
WAT = SPC
rather than "HOH = TP3" / "WAT = TP3" as the default seems to be, it seems
that this should direct TLEAP to look in the same solvents.lib file where
it finds the TIP3P parameters and find instead the SPC/E parameters and
put those in the topology wherever it finds water in the simulation.
The part I'm scratching my head about is that it DOES obtain the
correct charges (I've had to figure out what AMBER's unit conventions are
in that topology file, but I've verified that generating the topology with
"WAT = SPC" gives the charges I'd expect for SPC/E, and they are different
that those you get with "WAT = TP3"). But, TLEAP still inserts the TIP3P
parameters for Lennard Jones A and B coefficients, as well as bond
lengths--the TIP3P OH bond length is 0.9572, and this is still what I see
for the SPC/E topology, even though the OH bond length should be 1.0000.
I found this when I was trying to convert my own PDB, a box of 1728
water molecules, into a topology and coordinate files. However, when I
used a "solvateBox x SPCBOX 14.0" command in another study to solvate a
protein in SPC/E water, I find that I actually obtained similar
results--the charges in the topology were correct, but the bond lengths
remained those of TIP3P and the Lennard-Jones A and B coefficients were
also those of TIP3P, not SPC/E.
It seems that there is a major problem somewhere. Either I didn't know
about some subtle, additional command that I needed to insert to include
the rest of SPC/E water in the setup, in which case TLEAP needs to be made
more user-friendly, or there is some bug in TLEAP that makes it think that
SPC/E water has the same geometry and Lennard-Jones parameters as TIP3P (I
checked the solvents.lib file, and it has the correct geometry and LJ
parameters for both TIP3P and SPC/E).
The result is the same whether I use TLEAP from Amber8 or Amber9.
Please help!
Dave
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Received on Sun Jun 03 2007 - 06:07:39 PDT
