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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Received on Sun Feb 25 2018 - 11:30:02 PST
