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>
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]
> Sent: Sunday, February 25, 2018 3:55 PM
> To: 'Chris Neale' <candrewn.gmail.com>; 'AMBER Mailing List' <
> 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]
> Sent: Sunday, February 25, 2018 2:06 PM
> To: jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> ;
> AMBER Mailing List <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> > 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> ]
> Sent: Thursday, February 22, 2018 5:11 PM
> To: 'Daniel Roe' <daniel.r.roe.gmail.com <mailto:daniel.r.roe.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?
>
> 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> ]
> Sent: Thursday, February 22, 2018 3:20 PM
> To: James Kress <jimkress_58.kressworks.org <mailto:jimkress_58@
> kressworks.org> >; AMBER Mailing List <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> > 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>
> > 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 27 2018 - 11:00:02 PST
