Re: [AMBER] Water Geometry in SPCBOX Inconsistent with Literatures

From: David Cerutti <>
Date: Mon, 29 May 2017 04:24:54 -0400

This reminded me of an old problem whereby people (including advanced
users) could fail to source all the necessary files and get those chimeric
water models you are describing. However, in your case, I think you are
sourcing everything correctly. The fact is that SPCBOX is really TIP3PBOX
in terms of coordinates, just the parameters have been changed. What you
should see is that after one step of dynamics, the SPC/E water geometry
recovers. Check the bond and angle values in the generated PRMTOP and you
should also see SPC/E. You can use ${AMBERHOME}/bin/CheckMD -p <your
prmtop> -c <your inpcrd out of tleap> and then look in resID.txt to see a
description of each residue type in the system.

On Mon, May 29, 2017 at 3:30 AM, Changhao Wang <> wrote:

> 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
> frcmod.ionsjc_spce:
> 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 - 01:30:02 PDT
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