Is there a way I can track only a single acetonitrile molecule and its distance from the active site residues across the trajectory. In total my system has 200 acetonitrile molecules, just like we use mask for active site residues can we use a similar mask for tracking down only one solvent molecule and its movement using closest command?
________________________________
From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Sent: Saturday, March 23, 2019 1:39 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Closest command in cpptraj for non aqeous solvents
parm ACN_IL1B_solvated.prmtop
trajin ./prod/ACN_IL1B_production4K.mdcrd 1 3000
solvent .C3N
strip :WAT
closest 10 :1-153 first closestout closestmols.dat outprefix closest
run
I am just trying to find the closest 10 ACN molecules and my protein length is 153 residues.
CPPTRAJ: Trajectory Analysis. V4.12.1 (GitHub)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 03/22/19 16:05:58
| Available memory: 591.340 MB
INPUT: Reading input from 'STDIN'
[parm ACN_IL1B_solvated.prmtop]
Reading 'ACN_IL1B_solvated.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
[trajin ./prod/ACN_IL1B_production4K.mdcrd 1 3000]
Reading './prod/ACN_IL1B_production4K.mdcrd' as Amber NetCDF
[solvent .C3N]
Error: SetSolvent [ACN_IL1B_solvated.prmtop]: Mask .C3N selects no atoms.
[strip :WAT]
STRIP: Stripping atoms in mask [:WAT]
[closest 10 :1-153 first closestout closestmols.dat outprefix closest]
CLOSEST: Finding closest 10 solvent molecules to atoms in mask :1-153
Only first atom of solvent molecule used for distance calc.
Closest molecules will be saved to closestmols.dat
Stripped topology file will be written with prefix closest
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: ACN_IL1B_solvated.prmtop, 39605 atoms, 12325 res, box: Orthogonal, 12173 mol, 11955 solvent
INPUT TRAJECTORIES (1 total):
0: 'ACN_IL1B_production4K.mdcrd' is a NetCDF AMBER trajectory with coordinates, time, box, Parm ACN_IL1B_solvated.prmtop (Orthogonal box) (reading 3000 of 12500)
Coordinate processing will occur on 3000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'ACN_IL1B_solvated.prmtop' (2 actions):
0: [strip :WAT]
Stripping 35865 atoms.
Stripped topology: 3740 atoms, 370 res, box: Orthogonal, 218 mol
1: [closest 10 :1-153 first closestout closestmols.dat outprefix closest]
Warning: Parm ACN_IL1B_solvated.prmtop does not contain solvent.
Warning: Setup incomplete for [closest]: Skipping
----- ACN_IL1B_production4K.mdcrd (1-3000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 3000 frames and processed 3000 frames.
TIME: Avg. throughput= 621.4905 frames / second.
ACTION OUTPUT:
TIME: Analyses took 0.0000 seconds.
DATASETS (4 total):
CLOSEST_00001[Frame] "CLOSEST_00001[Frame]" (integer), size is 0
CLOSEST_00001[Mol] "CLOSEST_00001[Mol]" (integer), size is 0
CLOSEST_00001[Dist] "CLOSEST_00001[Dist]" (double), size is 0
CLOSEST_00001[FirstAtm] "CLOSEST_00001[FirstAtm]" (integer), size is 0
Total data set memory usage is at least 0.000 kB
DATAFILES (1 total):
closestmols.dat (Standard Data File): CLOSEST_00001[Frame] CLOSEST_00001[Mol] CLOSEST_00001[Dist] CLOSEST_00001[FirstAtm]
Warning: Set 'CLOSEST_00001[Frame]' contains no data.
Warning: Set 'CLOSEST_00001[Mol]' contains no data.
Warning: Set 'CLOSEST_00001[Dist]' contains no data.
Warning: Set 'CLOSEST_00001[FirstAtm]' contains no data.
Warning: File 'closestmols.dat' has no sets containing data.
RUN TIMING:
TIME: Init : 0.0001 s ( 0.00%)
TIME: Trajectory Process : 4.8271 s ( 99.97%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0002 s ( 0.00%)
TIME: Other : 0.0010 s ( 0.00%)
TIME: Run Total 4.8284 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 4.9431 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Saturday, March 23, 2019 1:02 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Closest command in cpptraj for non aqeous solvents
Hi,
To change the definition of 'solvent' for the 'closest' command,
please use the 'solvent' command just prior:
solvent <new solvent mask>
closest ...
Hope this helps,
-Dan
On Fri, Mar 22, 2019 at 3:23 PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> Hi All,
>
> I am trying to replicate some ideas given in https://doi.org/10.1002/cmdc.201100237
>
> [cid:3e994689-347c-4066-94a1-417766f31335]
> I have a protein in a water+acetonitrile co solvent box and I am trying to get the time series distance to be spitted out between the center of mass coordinates of the active site and the closest acetonitrile molecule. My system has 100 acetonitrile molecules and 3000 TIP3P waters.
> I have 4 plausible binding sites and I need to get a similar graph as this one to compute the distance between the closest acetonitrile and the binding site.
>
> Any ideas will be very helpful; as I found out the closest seems to identify water as solvent!
> Thanks
> Debarati
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Mar 22 2019 - 14:00:03 PDT
