[AMBER] Water Geometry in SPCBOX Inconsistent with Literatures

From: Changhao Wang <wchangha.uci.edu>
Date: Mon, 29 May 2017 00:30:23 -0700

Dear Developers,

I'm exploring to use the SPC/E water box as solvate my protein. However, I
found that SPCBOX added the TIP3P water molecules instead of SPC/E water.
I'm using Amber16. Here is what I did:

First I sourced ff14SB force field, and loaded frcmod.spce and

source leaprc.ff14SB.redq
loadamberparams frcmod.spce
loadamberparams frcmod.ionsjc_spce

Next I used solvateoct to add water:

solvateoct solute SPCBOX 8.0
saveamberparm solute solute.prmtop solute.inpcrd

It looks like the parameters in solute.prmtop are correct because it uses
charges and Lennard Jones coefficients from frcmod.spce.

However, the bonds and angles in solute.inpcrd file are not correct, but
are those of the TIP3P water: 0.957 angstrom and 104.52 degree respectively.
For SPC/E water, they should be 1.00 angstrom and 109.47 degree. Is there
anything wrong in my procedure?

All the best,
Changhao Wang
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Received on Mon May 29 2017 - 01:00:02 PDT
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