Sree,
to comment in addition to Arun's suspicion (visualization in VMD):
Did you use a pdb file or a parmtop/crd file pair for visualization?
If you used the former, try the later, since the pdb file format has
known limitations (e.g. maximum coordinate values or maximum residue
numbers). Maybe a look into the pdb file solves your problem as a
visualization issue only, since the "truth" (from an Amber point of
view) is in the top/crd files, which are used for simulation, not in the
pdb file.
Maybe that helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 12.01.26 um 10:00 schrieb Arun Srikanth via AMBER:
> This could be a visualization problem with vmd. Have you done a hard check
> ? I.e., check whether the difference in max and min of coordinates is less
> than the box dim ?
>
> On Mon, 12 Jan 2026, 07:23 Arun Srikanth, <askforarun.gmail.com> wrote:
>
>> How are you visulizing the box, i mean what software ?
>>
>> Arun
>>
>> On Mon, 12 Jan 2026, 07:02 Sree Gouri Menon via AMBER, <amber.ambermd.org>
>> wrote:
>>
>>> Dear AMBER users,
>>>
>>> I am encountering an issue with solvation box generation in tleap and
>>> would
>>> appreciate some guidance.
>>>
>>> I am studying aggregation and have placed 10 copies of my molecule in a
>>> box
>>> to create the initial configuration. After loading this system into tleap
>>> and adding water and ions, the solvation box generated by tleap does not
>>> fully enclose all 10 molecules. In particular, 1–2 molecules extend
>>> outside
>>> the box boundaries, and the box itself appears poorly positioned relative
>>> to the solute.
>>>
>>> I have tried increasing the solvation box size (using larger buffer
>>> distances / box dimensions), but the problem persists — the box still does
>>> not accommodate all molecules. This is confusing because the original
>>> structures were generated inside a cubic box of ~15 nm per side, and the
>>> solvation box dimensions I specify in tleap are larger than this. I have
>>> attached an image showing the issue for clarity.
>>>
>>> Is there a recommended workflow to ensure that all molecules are properly
>>> enclosed before solvation (e.g., recentering, resetting the unit cell, or
>>> specific tleap commands)?
>>>
>>> Any suggestions or pointers would be greatly appreciated.
>>>
>>> Thank you for your time and help.
>>>
>>> Best regards,
>>> Sree Gouri
>>> [image: image.png]
>>>
>>> --
>>> The information contained in this electronic communication is intended
>>> solely for the individual(s) or entity to which it is addressed. It may
>>> contain proprietary, confidential and/or legally privileged information.
>>> Any review, retransmission, dissemination, printing, copying or other use
>>> of, or taking any action in reliance on the contents of this information
>>> by
>>> person(s) or entities other than the intended recipient is strictly
>>> prohibited and may be unlawful. If you have received this communication
>>> in
>>> error, please notify us by responding to this email or telephone and
>>> immediately and permanently delete all copies of this message and any
>>> attachments from your system(s). The contents of this message do not
>>> necessarily represent the views or policies of BITS Pilani.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 12 2026 - 06:30:02 PST
