On Wed, Mar 26, 2014, MOHD HOMAIDUR RAHMAN wrote:
> source leaprc.ff99bsc0
> WAT = SPC
> HOH = SPC
> loadAmberParms frcmod.spce
> set SPC.1 name "SPC"
Why did you do this? It might well have some undesirable side-effects; waters
are conventionally named WAT or HOH.
> set default FlexibleWater on
This is probably pretty bad: SPC/E is a rigid water model, not a flexible one.
> RM = loadpdb wat_pack.pdb
What are the residue names in the wat_pack.pdb file?
> By searching SPC/E water model parameter in topology file, I found that the
> leap taken the default TIP3P water model parameter.
I don't immediately see why this would be happening; the one big unknown here
is the contents of your pdb-file, so let's rule out problems there first.
(Maybe some other eagle-eyed person on the list will spot the problem first)
...dac
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Received on Wed Mar 26 2014 - 13:00:03 PDT
