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>
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]
> Sent: Thursday, February 22, 2018 5:11 PM
> To: 'Daniel Roe' <daniel.r.roe.gmail.com>; 'AMBER Mailing List' <
> 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]
> Sent: Thursday, February 22, 2018 3:20 PM
> To: James Kress <jimkress_58.kressworks.org>; AMBER Mailing List <
> 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>
> 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
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Feb 25 2018 - 11:30:02 PST
