Hi,
On Fri, Mar 22, 2019 at 4:09 PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
> [solvent .C3N]
> Error: SetSolvent [ACN_IL1B_solvated.prmtop]: Mask .C3N selects no atoms.
You need to fix the mask you are providing to 'solvent'. Did you mean
':C3N' maybe?
-Dan
> [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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 26 2019 - 09:00:03 PDT
