Hi Patricio,
Very standard script, pasted at the bottom below. So we haven't been using
the iso/aniso options. As you can see we are using the ff19SB and OPC water
combo. As I mentioned, this same script run through multiple versions of
amber only starts adding a large number of extra waters when we hit the
amber26 version. As you can see the AmberTools25 and AmberTools23 versions
of tleap both give a smaller number of OPC water residues added, and the
bottom of the rst7 file for each of these agree identically. It is only in
AmberTools26 where things start to change. Thanks for your help looking
into this! - Joe
For example when I use AmberTools26 it gives me:
Loading PDB file: ../../00-structure/fold_full_sequence_model_0.pdb
total atoms in file: 5271
Leap added 4881 missing atoms according to residue templates:
4881 H / lone pairs
Scaling up box by a factor of 1.260286 to meet diagonal cut criterion
Solute vdw bounding box: 137.890 98.975 70.390
Total bounding box for atom centers: 209.069 209.069 209.069
(box expansion for 'iso' is 81.5%)
Solvent unit box: 18.865 18.478 19.006
Volume: 4635036.174 A^3 (oct)
Total mass 2620962.702 amu, Density 0.939 g/cc
Added 141329 residues.
and then the bottom of the rst7 is: 181.9246991 181.9246991 181.9246991
109.4712190 109.4712190 109.4712190
For example when I use AmberTools25 it gives me:
Loading PDB file: ../../00-structure/fold_full_sequence_model_0.pdb
total atoms in file: 5271
Leap added 4881 missing atoms according to residue templates:
4881 H / lone pairs
Scaling up box by a factor of 1.464352 to meet diagonal cut criterion
Solute vdw bounding box: 137.890 98.975 70.390
Total bounding box for atom centers: 178.892 178.892 178.892
(box expansion for 'iso' is 105.2%)
Solvent unit box: 18.865 18.478 19.006
Volume: 2910739.196 A^3 (oct)
Total mass 1628046.894 amu, Density 0.929 g/cc
Added 86216 residues.
and then the bottom of the rst7 is: 155.7907688 155.7907688 155.7907688
109.4712190 109.4712190 109.4712190
For example when I use AmberTools23 it gives me:
Loading PDB file: ../../00-structure/fold_full_sequence_model_0.pdb
total atoms in file: 5271
Leap added 4881 missing atoms according to residue templates:
4881 H / lone pairs
Scaling up box by a factor of 1.464352 to meet diagonal cut criterion
Solute vdw bounding box: 137.890 98.975 70.390
Total bounding box for atom centers: 178.892 178.892 178.892
(box expansion for 'iso' is 105.2%)
Solvent unit box: 18.865 18.478 19.006
Volume: 2910739.196 A^3 (oct)
Total mass 1628046.894 amu, Density 0.929 g/cc
Added 86216 residues.
and then the bottom of the rst7 is: 155.7907688 155.7907688 155.7907688
109.4712190 109.4712190 109.4712190
----SCRIPT----
#Load in the necessary forcefields
source leaprc.protein.ff19SB
source leaprc.water.opc
#Load the PDBs
prot = loadpdb ../00-structure/fold_full_sequence_model_0.pdb
#solvate system
solvateoct prot OPCBOX 14
#Adding Ions
addIonsRand prot Na+ 0
addIonsRand prot Cl- 0
#save files
saveAmberParm prot sys.parm7 sys.rst7
# Quit
quit
------
Joseph Baker, PhD
Barbara Meyers Pelson Chair in Faculty-Student Engagement (AY 2024-2027)
Professor, Department of Chemistry
The College of New Jersey
Ewing, NJ 08628
Chair-elect (2026), Trenton Local Section of the ACS
Chemistry Division Representative (2024-2027), The Council on Undergraduate
Research
On Tue, Jun 16, 2026 at 3:46 PM Patricio Barletta via AMBER <
amber.ambermd.org> wrote:
> *
> Can I see the tleap script you are running? I'm curious about the water
> model.
> *
> If you do tail -n1 <OUTPUT RST7 FILE> , do you get the same box size in
> all cases?
> *
> If you run NVT on the output systems, do you get the same starting density?
>
> The coordinates for the pre-equilibrated water molecules are at
> `amber/dat/leap/lib/`, and I don't see any change on files like
> 'tip3pbox.off'.
> The other factor that may affect the final result is the usage of the
> keyword "aniso", that prevents tleap from centering and reorienting the
> solute before adding the box. This increases the box size for a given
> buffer length.
>
> Best,
>
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> 1. solvateoct behavior in Amber26 (Baker, Joseph)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 16 Jun 2026 14:55:03 -0400
> From: "Baker, Joseph" <bakerj.tcnj.edu>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] solvateoct behavior in Amber26
> Message-ID:
> <
> CAA5VDpDSCstP8vGa_cQ3Nj9eWtZCx3vpwkNSvTuWcxJsukYpTw.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
>
> One of my students noticed that their simulations were running much more
> slowly suddenly, and when looking at our tleap output we observed that the
> solvateoct command seems to be adding a significantly larger number of
> water molecules to the system than it has in the past (with the same
> padding value, using the same initial structure). We went back and checked
> the behavior in 25,24,23,22 versions and they were all consistent with the
> number of water molecules being placed by solvateoct. Has there been some
> change in the way solvateoct handles building the water shell?
>
> Thanks!
> Joe
>
> ------
> Joseph Baker, PhD
> Barbara Meyers Pelson Chair in Faculty-Student Engagement (AY 2024-2027)
> Professor, Department of Chemistry
> The College of New Jersey
> Ewing, NJ 08628
> Chair-elect (2026), Trenton Local Section of the ACS
> Chemistry Division Representative (2024-2027), The Council on Undergraduate
> Research
>
>
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