Hi Dan,
Yes, I have checked the trajectory, pdb created in tleap step (after water
addition), and your suggestion to check resinfo.
All these confirm that indeed there are waters with resname WAT in the
trajectory (truncated output of resinfo :WAT for loaded trajectory in
cpptraj is given below).
Thus it is strange that :WAT mask is not working as expected.
Nonetheless, I ran the watershell command in cpptraj and it gives an output
like the following.
Thus I'm interpreting this such that
the 44 K+ ions are bonded to 311 waters in total for the first hydration
shell that within 3A and
within 5A there are 779 i.e. 779 - 311 = 468 waters are in the second
hydration shell.
This gives 311/44 = 7 water per K+ ion in the first frame.
Avg for 2000 frames is 7.29.
I think these numbers are meaningful and show give the analysis I want.
Please let me know what you think.
thank you and best regards
CPPTRAJ: Version V4.14.0 (AmberTools V19.11)
$ head 1bvy-af-KWATshell.dat
#Frame WS_00001[lower] WS_00001[upper]
1 311 779
2 318 769
3 314 779
4 316 787
5 325 782
6 308 792
7 325 791
8 312 811
23270 WAT 77554 77556 3 23270 22658
23271 WAT 77557 77559 3 23271 22659
23272 WAT 77560 77562 3 23272 22660
23273 WAT 77563 77565 3 23273 22661
23274 WAT 77566 77568 3 23274 22662
23275 WAT 77569 77571 3 23275 22663
23276 WAT 77572 77574 3 23276 22664
23277 WAT 77575 77577 3 23277 22665
23278 WAT 77578 77580 3 23278 22666
23279 WAT 77581 77583 3 23279 22667
23280 WAT 77584 77586 3 23280 22668
23281 WAT 77587 77589 3 23281 22669
23282 WAT 77590 77592 3 23282 22670
23283 WAT 77593 77595 3 23283 22671
23284 WAT 77596 77598 3 23284 22672
23285 WAT 77599 77601 3 23285 22673
23286 WAT 77602 77604 3 23286 22674
23287 WAT 77605 77607 3 23287 22675
>
> watershell :K+ out 1bvy-af-KWATshell.dat
[watershell :K+ out 1bvy-af-KWATshell.dat]
WATERSHELL: Output to 1bvy-af-KWATshell.dat
The first shell will contain solvent < 3.400 angstroms from
the solute; the second shell < 5.000 angstroms...
Solute atoms will be specified by [:K+]
# solvent molecules in 'lower' shell stored in set 'WS_00001[lower]'
# solvent molecules in 'upper' shell stored in set 'WS_00001[upper]'
> run
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: 1bvy-af-solv.prmtop, 77607 atoms, 23287 res, box: Orthogonal, 22675
mol, 22614 solvent
INPUT TRAJECTORIES (1 total):
0: '1bvy-af-solv-prod.nc' is a NetCDF AMBER trajectory with coordinates,
time, box, Parm 1bvy-af-solv.prmtop (Orthogonal box) (reading 2000 of 2000)
Coordinate processing will occur on 2000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '1bvy-af-solv.prmtop' (1 actions):
0: [watershell :K+ out 1bvy-af-KWATshell.dat]
Mask [:K+] corresponds to 44 atoms.
Selecting all solvent atoms (67842 total)
Imaging is on.
----- 1bvy-af-solv-prod.nc (1-2000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 2000 frames and processed 2000 frames.
TIME: Avg. throughput= 26.3706 frames / second.
ACTION OUTPUT:
TIME: Analyses took 0.0000 seconds.
DATASETS (2 total):
WS_00001[lower] "WS_00001[lower]" (integer), size is 2000 (8.000 kB)
WS_00001[upper] "WS_00001[upper]" (integer), size is 2000 (8.000 kB)
Total data set memory usage is at least 16.000 kB
DATAFILES (1 total):
1bvy-af-KWATshell.dat (Standard Data File): WS_00001[lower]
WS_00001[upper]
RUN TIMING:
TIME: Init : 0.0003 s ( 0.00%)
TIME: Trajectory Process : 75.8420 s ( 99.99%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0044 s ( 0.01%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 75.8469 s
---------- RUN END ---------------------------------------------------
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
https://niperguwahati.ac.in/DOC/profile/dixit.pdf
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
Please consider the environment before printing this e-mail
On Thu, Jan 13, 2022 at 7:13 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Jan 13, 2022 at 1:39 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
> > I want to find the number of water molecules that are in direct contact
> > with the K+ ions in each frame during the simulation. I think this is
> not
>
> Off the top of my head, I would try either the 'watershell' command
> (which will do a simple distance-cutoff-based count of waters near
> specified atoms, in this case your ions) or the 'hbond' command
> specifying the ions and using the solventdonor/solventacceptor
> keywords.
>
> > nativecontacts name KWAT :K+ :WAT byresidue out KWATcontacts.dat mindist
> > maxdist distance 4.0 first map mapout KWATresmap.gnu
> > contactpdb KWATcontactmap.pdb series seriesout KWATnativecontacts.dat
> > writecontacts KWATwritecontacts.dat
> >
> > Mask [:K+] corresponds to 145 atoms.
> > Mask [:WAT] corresponds to 0 atoms.
>
> Are you absolutely certain the topology you have has water in it? And
> if so, are you sure it's called WAT? I ask because a mask parser
> failure would be very unusual. What happens if you just load the
> topology and type "resinfo :WAT"? Also, it would be helpful to know
> the version of cpptraj you are using.
>
> -Dan
>
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Received on Thu Jan 13 2022 - 07:00:02 PST
