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

From: Chris Moth <>
Date: Tue, 30 May 2017 11:57:04 -0500

Yes to David's reply.

The "old problem" is one that has frustrated me at various deeply
annoying junctures!

Changhao noted he is using Amber16.

In Amber16, there is a single command that can be used , a welcome

     source leaprc.water.spce

I'd also encourage him and others to carefully read the latest manual
"3. Molecular mechanics force fields" as it notes ...... "*we have
implemented a new scheme* for users to specify the force fields they
wish to use..."

On 5/29/2017 3:24 AM, David Cerutti wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
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Received on Tue May 30 2017 - 10:00:02 PDT
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