Hi Jim,
Regarding qmmask: It should work like any other Amber mask. You should be able to select any atoms or residues with qmmask - whether that makes physical sense is a different question. What you try to achieve (single point calculations of a few residues surrounded by water molecules) makes sense and should work.
I am surprised that you get different results for the qmmask selection and using ambmask. Does your selection work for e.g. restraintmask?
I tried using :WAT in qmmask for a system I have lying around and it works just fine. I tried qmmask = ‘:1-6&:WAT’ for a system in which residues 1 to 3 are not water, and sander correctly selected residues 4 to 6 for the QM region.
Regarding QM_CHECK_PERIODIC: The QM region boundaries extended by qmcut in each direction must fit into your simulation box (this is checked with the QM region translated to the center of the simulation box). Otherwise you would include MM charges multiple times in your QM Hamiltonian. If the code bails out you must use a larger simulation box or, if this is an option, reduce qmcut.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Feb 27, 2018, at 12:01 PM, James Kress <jimkress_58.kressworks.org> wrote:
>
> Carlos,
>
>
>
> Thanks for your reply.
>
>
>
> 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.
>
>
>
> I’ll repost this email under the heading of “Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error”. Perhaps that will get the attention of someone who will help.
>
>
>
> Thanks again.
>
>
>
> 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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>
>
>
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Received on Tue Feb 27 2018 - 18:00:04 PST
