I have an oligomer of DNA that has been solvated, charge neutralized and equilibrated. I am trying to do QM/MM (on a single frame from the equilibration run) where the QM region consists of the six residues in the center of the DNA, the 6 nearest Na+ ions and then the shell of water immediately adjacent to the six residues and Na+ ions of interest. All the atoms outside the QM region are left as MM atoms.
From my reading of the user’s guide, solvent can be in the QM region, it appears that this could be done using &vsolv. However, when I try that I get the dreaded (and unresolved to the best of my knowledge) “SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f> QM region + cutoff larger than box cannot continue, need larger box.” error.
So, to avoid that bug I decided to try to use qmmask to specify the QM region. Given the fact that the masks I am trying to use work just fine with ambmask, I thought they would be fine in SANDER but apparently, I was incorrect.
So, unless there is a fix for QM_CHECK_PERIODIC or qmmask I have no hope of using Amber to perform the calculations of interest.
Thanks.
Jim
From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
Sent: Tuesday, February 27, 2018 1:55 PM
To: jimkress_58.kressworks.org; AMBER Mailing List <amber.ambermd.org>
Cc: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
Jim,
I don't have any concrete suggestions since I don't work with the QM/MM code, but a quick read of your tests makes it look to me like the problem isn't the mask itself, it's whether the QM/MM code is designed to work with solvents (or mobile ions) in the QM region. Based on the region+cutoff error, I suspect that this was not part of the code design. I think usually people have a QM region that is embedded in a larger MM, rather than QM perhaps scattered throughout as would happen when your solvent or ions diffuse during MD. Am I understanding properly what you are trying to do?
It might help you get more discussion here if you change the subject to something related to whether solvent can be in the QM region of a QM/MM run since that may trigger recognition in someone reading the email subjects....
best,
Carlos
On Tue, Feb 27, 2018 at 1:48 PM, James Kress <jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> > wrote:
Is anyone in the Amber group looking into this bug? If it's not going to be fixed, please let me know so I can move on and work with other software.
Thank you.
Jim Kress
From: James Kress [mailto:jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> ]
Sent: Sunday, February 25, 2018 3:55 PM
To: 'Chris Neale' <candrewn.gmail.com <mailto:candrewn.gmail.com> >; 'AMBER Mailing List' <amber.ambermd.org <mailto:amber.ambermd.org> >
Subject: RE: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
Chris,
Thanks for the suggestion. I’ll have to run ambmask first (since it works properly) and then process the resulting pdb and/or the “short” output file to get the atom numbers and store them in the proper format for use in the qmmask command.
Then I’ll have to hope that the dreaded “SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f> QM region + cutoff larger than box cannot continue, need larger box.” error does not occur since it appears there is no fix for that either, except to rerun all my simulations in a different style box. The appropriate box style is not documented so I’ll have to experiment with a variety to get the best choice that does not generate the QM_CHECK_PERIODIC<qm_mm.f> error message.
Jim
From: Chris Neale [mailto:candrewn.gmail.com <mailto:candrewn.gmail.com> ]
Sent: Sunday, February 25, 2018 2:06 PM
To: jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> <mailto:jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> > ; AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org> <mailto:amber.ambermd.org <mailto:amber.ambermd.org> > >
Subject: Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
One possible workaround is preliminary bash scripting on the input structure file to get a list of residue numbers in "WAT" and use that?
On Sun, Feb 25, 2018 at 12:03 PM, James Kress <jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> <mailto:jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> > > wrote:
Any ideas on how to fix the problems I have reported? Their existence has brought my work to a screeching halt. I cannot proceed until there is a fix or a workaround.
Thanks.
Jim
-----Original Message-----
From: James Kress [mailto:jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> <mailto:jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> > ]
Sent: Thursday, February 22, 2018 5:11 PM
To: 'Daniel Roe' <daniel.r.roe.gmail.com <mailto:daniel.r.roe.gmail.com> <mailto:daniel.r.roe.gmail.com <mailto:daniel.r.roe.gmail.com> > >; 'AMBER Mailing List' <amber.ambermd.org <mailto:amber.ambermd.org> <mailto:amber.ambermd.org <mailto:amber.ambermd.org> > >
Subject: RE: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
Hi Dan,
Thanks for your reply. I eliminated all white space from the qmmask entry (including trailing white space).
I tried:
qmmask=':5-7,16-18|(:5-7,16-18<:5&:WAT)|(:5-7,16-18<:9&:Na+)',
and got:
LOADING THE QUANTUM ATOMS AS GROUPS
Mask :5-7,16-18|(:5-7,16-18<:5&:WAT)|(:5-7,16-18<:9&:Na+); matches 17964 atoms
PARAMETER RANGE CHECKING:
parameter QMMM: (number of quantum atoms) has value 17964
This is outside the legal range
Lower limit: 1 Upper limit: 10000
The limits may be adjustable; search in the .h files
I got the same result with:
qmmask='(:5-7,16-18)|(:5-7,16-18<:5&:WAT)|(:5-7,16-18<:9&:Na+)',
qmmask=':5-7,16-18|:5-7,16-18<:5&:WAT|:5-7,16-18<:9&:Na+',
qmmask='(:5-7,16-18<:5&:WAT)|(:5-7,16-18<:9&:Na+)|(:5-7,16-18)',
If I try:
qmmask='(:5-7,16-18<:5&:WAT)|(:5-7,16-18<:9&:Na+)',
I get
LOADING THE QUANTUM ATOMS AS GROUPS
Mask (:5-7,16-18<:5&:WAT)|(:5-7,16-18<:9&:Na+); matches 17772 atoms
PARAMETER RANGE CHECKING:
parameter QMMM: (number of quantum atoms) has value 17772
This is outside the legal range
Lower limit: 1 Upper limit: 10000
The limits may be adjustable; search in the .h files
If I try:
qmmask='(:5-7,16-18)|(:5-7,16-18<:9&:Na+)',
I get:
LOADING THE QUANTUM ATOMS AS GROUPS
Mask (:5-7,16-18)|(:5-7,16-18<:9&:Na+); matches 232 atoms
BOX TYPE: TRUNCATED OCTAHEDRON
Which is OK until the job bombs with a different problem:
SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f> QM region + cutoff larger than box cannot continue, need larger box.
So, ignoring the QM_CHECK_PERIODIC then I try:
qmmask='(:5-7,16-18)|(:5-7,16-18<:5&:WAT)',
And get:
LOADING THE QUANTUM ATOMS AS GROUPS
Mask :5-7,16-18|(:5-7,16-18<:5&:WAT); matches 17924 atoms
PARAMETER RANGE CHECKING:
parameter QMMM: (number of quantum atoms) has value 17924
This is outside the legal range
Finally, I try:
qmmask='(:5-7,16-18<:5&:WAT)',
And get:
LOADING THE QUANTUM ATOMS AS GROUPS
Mask (:5-7,16-18<:5&:WAT); matches 17732 atoms
PARAMETER RANGE CHECKING:
parameter QMMM: (number of quantum atoms) has value 17732
This is outside the legal range
It would appear the presence of WAT in qmmask is the issue.
Any suggestions on how I can fix this?
Thanks.
Jim
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com <mailto:daniel.r.roe.gmail.com> <mailto:daniel.r.roe.gmail.com <mailto:daniel.r.roe.gmail.com> > ]
Sent: Thursday, February 22, 2018 3:20 PM
To: James Kress <jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> <mailto:jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> > >; AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org> <mailto:amber.ambermd.org <mailto:amber.ambermd.org> > >
Subject: Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
Hi,
Try removing all whitespace from your mask string.
-Dan
On Thu, Feb 22, 2018 at 2:58 PM, James Kress <jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> <mailto:jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> > > wrote:
> As I have reported previously, ambmask and qmmask give different
> results for identical inpcrd, prmtop, and mask inputs.
>
> ambmask
>
> ambmask -p prmtop -c inpcrd -find ':5-7,16-18 |
> (:5-7,16-18
> <:5.0 & :WAT) | (:5-7,16-18 <:9.0 & :Na+)'
>
> I get 379 atoms selected. I get 6 Na+, 176 WAT (44
> water molecules), and the balance are the DNA residues.
>
> qmmask
>
> qmmask=':5-7,16-18 | (:5-7,16-18 <:5.0 & :WAT) |
> (:5-7,16-18
> <:9.0 & :Na+)',
>
> Yields 17964, atoms where all the additional atoms (in
> excess of the 379 found by ambmask) are from all the WATs being included.
>
> This is confirmed by using:
>
> qmmask=':5-7,16-18 | (:5-7,16-18 <:9.0 & :Na+)',
>
> which recovers the residues and Na+ found with ambmask
>
> Also, if I try
>
> qmmask=':5-7,16-18 | (:5-7,16-18 <:5.0 & :WAT)',
>
> I get the residues and all the WATs
>
> And when I do
>
> qmmask='(:5-7,16-18 <:5.0 & :WAT)',
>
> I just get all the WATs with no residues
>
> I've looked through the mailing list archives and have seen this
> problem reported previously. However, I could not find any solution
> in the archives.
>
> Any ideas why Amber16 has these problems with qmmask and WAT?
>
> Thanks.
>
> Jim Kress
>
>
> _______________________________________________
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Feb 27 2018 - 12:30:03 PST
