Hi Jim,
Can you send us a test case where this happens?
From reading your e-mail, it looks as QM region is getting way too large. It may be that some of the water or Na+ is getting far from the central residues such that the position of this atom + cutoff is larger than the box, but it would be better to look at a working (in this case, not-working) example.
Regards,
—
Gustavo Seabra.
> Em 27 de fev de 2018, à(s) 17:02, James Kress <jimkress_58.kressworks.org> escreveu:
>
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org <mailto:AMBER.ambermd.org> <mailto:AMBER.ambermd.org <mailto:AMBER.ambermd.org> >
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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
