Hi Dan,
This is the list of output files I generate
-rw-r--r--. 1 debarati users 880354 Mar 27 09:59 contacts.out
-rw-r--r--. 1 debarati users 1080325 Mar 27 09:59 native.gnu
-rw-r--r--. 1 debarati users 1080328 Mar 27 09:59 nonnative.gnu
-rw-r--r--. 1 debarati users 303021 Mar 27 09:59 nn_contact.pdb
-rw-r--r--. 1 debarati users 135 Mar 27 09:59 nativecontacts.dat
-rw-r--r--. 1 debarati users 303021 Mar 27 09:59 contacts.pdb
the B factor column in contacts.pdb and nn_contact.pdb have -nan values, which I do not know how to interpret!
The contents of nativecontacts.dat file is
# Contacts: Contacts_00002
# Native contacts determined from mask ':275' and mask ':90,99,95,96'
# Non-native Contacts: Contacts_00002
~
~
Debarati
Postdoctoral research fellow
College of Pharmacy
University of Michigan, USA
________________________________
From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Sent: Wednesday, March 27, 2019 3:24 AM
To: AMBER Mailing List
Subject: Re: [AMBER] locating the single probe out of 80000 snapshots
Also what should be my reference structure in this case ?
Debarati
Postdoctoral research fellow
College of Pharmacy
University of Michigan, USA
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Wednesday, March 27, 2019 3:23 AM
To: AMBER Mailing List
Subject: Re: [AMBER] locating the single probe out of 80000 snapshots
Hi,
On Wed, Mar 27, 2019 at 9:13 AM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
> I am trying to select 3 residues with which ACN 275 kind of interacts but I am getting errors.
What are the exact errors/error messages?
> Can you please tell me how to account for 3 residues (Res 90, Res 99, Res 62 of the protein) in the second mask for nativecontacts?
Should be able to just add a mask that encompasses these residues:
nativecontacts :275 :90,99,62 ...
-Dan
>
> Thanks
>
>
> Debarati
> Postdoctoral research fellow
> College of Pharmacy
> University of Michigan, USA
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Tuesday, March 26, 2019 2:36 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] locating the single probe out of 80000 snapshots
>
> Hi,
>
> On Tue, Mar 26, 2019 at 5:05 PM Debarati DasGupta
> <debarati_dasgupta.hotmail.com> wrote:
> > nativecontacts :275 writecontacts nativecontacts.dat resout res noimage distance 4.0 out contacts.out first resoffset 4 contactpdb contacts.pdb byresidue map mapout gnu series seriesout nativeseries.dat savenonnative seriesnnout nn.dat nncontactpdb nn_contact.pdb
> > go
> >
> > I am trying to track the contacts of my 275th Acetonitrile molecule (there are 200 ACN molecules numbered 154 to 354) and I kind of found that ACN 275, ACN 185 are the ones which reside in the binding spot based on xplor density grid calculations.
>
> I think you may want a second mask here that selects the protein, so
> you can actually track the contacts that residue 275 makes (unless I'm
> not really understanding what you want to do).
>
> -Dan
>
> >
> >
> > I get this message from cpptraj =====>
> >
> >
> > CPPTRAJ: Trajectory Analysis. V4.12.1 (GitHub)
> > ___ ___ ___ ___
> > | \/ | \/ | \/ |
> > _|_/\_|_/\_|_/\_|_
> >
> > | Date/time: 03/26/19 17:06:47
> > | Available memory: 951.022 MB
> >
> > INPUT: Reading input from 'STDIN'
> > [parm ../run_1/ACN_IL1B_solvated.prmtop]
> > Reading '../run_1/ACN_IL1B_solvated.prmtop' as Amber Topology
> > Radius Set: modified Bondi radii (mbondi)
> > [trajin ../run_1/prod/ACN_IL1B_production4A.mdcrd 1 1250 1]
> > Reading '../run_1/prod/ACN_IL1B_production4A.mdcrd' as Amber NetCDF
> > [trajin ../run_1/prod/ACN_IL1B_production4B.mdcrd 1 1250 1]
> > Reading '../run_1/prod/ACN_IL1B_production4B.mdcrd' as Amber NetCDF
> > [trajin ../run_1/prod/ACN_IL1B_production4C.mdcrd 1 1250 1]
> > Reading '../run_1/prod/ACN_IL1B_production4C.mdcrd' as Amber NetCDF
> > [trajin ../run_1/prod/ACN_IL1B_production4D.mdcrd 1 1250 1]
> > Reading '../run_1/prod/ACN_IL1B_production4D.mdcrd' as Amber NetCDF
> > [trajin ../run_1/prod/ACN_IL1B_production4E.mdcrd 1 1250 1]
> > Reading '../run_1/prod/ACN_IL1B_production4E.mdcrd' as Amber NetCDF
> > [trajin ../run_1/prod/ACN_IL1B_production4F.mdcrd 1 1250 1]
> > Reading '../run_1/prod/ACN_IL1B_production4F.mdcrd' as Amber NetCDF
> > [trajin ../run_1/prod/ACN_IL1B_production4G.mdcrd 1 1250 1]
> > Reading '../run_1/prod/ACN_IL1B_production4G.mdcrd' as Amber NetCDF
> > [trajin ../run_1/prod/ACN_IL1B_production4H.mdcrd 1 1250 1]
> > Reading '../run_1/prod/ACN_IL1B_production4H.mdcrd' as Amber NetCDF
> > [autoimage]
> > AUTOIMAGE: To box center based on center of mass, anchor is first molecule.
> > [reference ../run_1/ACN_IL1B_allmin.rst]
> > Reading '../run_1/ACN_IL1B_allmin.rst' as Amber NC Restart
> > Setting active reference for distance-based masks: 'ACN_IL1B_allmin.rst'
> > [nativecontacts :275 writecontacts nativecontacts.dat resout res noimage distance 4.0 out contacts.out first resoffset 4 contactpdb contacts.pdb byresidue map mapout gnu series seriesout nativeseries.dat savenonnative seriesnnout nn.dat nncont actpdb nn_contact.pdb]
> > NATIVECONTACTS: Mask1=':275', native contacts set up based on first frame.
> > Contacts will be ignored for residues spaced < 5 apart.
> > Map will be printed by residue.
> > Saving non-native contacts as well (may use a lot of memory).
> > Distance cutoff is 4 Angstroms, imaging is off.
> > Mask selection will not include solvent.
> > Data set name: Contacts_00002
> > Output to 'contacts.out'
> > Contact stats will be written to 'nativecontacts.dat'
> > Contact res pairs will be written to 'res'
> > Contact PDB will be written to 'contacts.pdb'
> > Non-native contact PDB will be written to 'nn_contact.pdb'
> > Native contacts map will be saved as set 'Contacts_00002[nativemap]'
> > Non-native contacts map will be saved as set 'Contacts_00002[nonnatmap]'
> > Native map output to 'native.gnu'
> > Native map output to 'nonnative.gnu'
> > Saving native contact time series Contacts_00002[NC].
> > Writing native contact time series to nativeseries.dat
> > Saving non-native contact time series Contacts_00002[NN]
> > Writing non-native contact time series to nn.dat
> > [go]
> > ---------- RUN BEGIN -------------------------------------------------
> >
> > PARAMETER FILES (1 total):
> > 0: ACN_IL1B_solvated.prmtop, 39605 atoms, 12325 res, box: Orthogonal, 12173 mol, 11955 solvent
> >
> > INPUT TRAJECTORIES (8 total):
> > 0: 'ACN_IL1B_production4A.mdcrd' is a NetCDF AMBER trajectory with coordinates, time, box, Parm ACN_IL1B_solvated.prmtop (Orthogonal box) (reading 1250 of 1250)
> > 1: 'ACN_IL1B_production4B.mdcrd' is a NetCDF AMBER trajectory with coordinates, time, box, Parm ACN_IL1B_solvated.prmtop (Orthogonal box) (reading 1250 of 1250)
> > 2: 'ACN_IL1B_production4C.mdcrd' is a NetCDF AMBER trajectory with coordinates, time, box, Parm ACN_IL1B_solvated.prmtop (Orthogonal box) (reading 1250 of 1250)
> > 3: 'ACN_IL1B_production4D.mdcrd' is a NetCDF AMBER trajectory with coordinates, time, box, Parm ACN_IL1B_solvated.prmtop (Orthogonal box) (reading 1250 of 1250)
> > 4: 'ACN_IL1B_production4E.mdcrd' is a NetCDF AMBER trajectory with coordinates, time, box, Parm ACN_IL1B_solvated.prmtop (Orthogonal box) (reading 1250 of 1250)
> > 5: 'ACN_IL1B_production4F.mdcrd' is a NetCDF AMBER trajectory with coordinates, time, box, Parm ACN_IL1B_solvated.prmtop (Orthogonal box) (reading 1250 of 1250)
> > 6: 'ACN_IL1B_production4G.mdcrd' is a NetCDF AMBER trajectory with coordinates, time, box, Parm ACN_IL1B_solvated.prmtop (Orthogonal box) (reading 1250 of 1250)
> > 7: 'ACN_IL1B_production4H.mdcrd' is a NetCDF AMBER trajectory with coordinates, time, box, Parm ACN_IL1B_solvated.prmtop (Orthogonal box) (reading 1250 of 1250)
> > Coordinate processing will occur on 10000 frames.
> >
> > REFERENCE FRAMES (1 total):
> > 0: ACN_IL1B_allmin.rst:1
> > Active reference frame for distance-based masks is 'default_name'
> >
> > BEGIN TRAJECTORY PROCESSING:
> > .....................................................
> > ACTION SETUP FOR PARM 'ACN_IL1B_solvated.prmtop' (2 actions):
> > 0: [autoimage]
> > Using first molecule as anchor.
> > 217 molecules are fixed to anchor: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 1 40 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 18
0 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 20 1 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218
> > 11955 molecules are mobile.
> > 1: [nativecontacts :275 writecontacts nativecontacts.dat resout res noimage distance 4.0 out contacts.out first resoffset 4 contactpdb contacts.pdb byresidue map mapout gnu series seriesout nativeseries.dat savenonnative seriesnnout nn.dat nnc ontactpdb nn_contact.pdb]
> > Mask [:275] corresponds to 6 atoms.
> > 6 potential contact sites for ':275'
> > Imaging disabled.
> > ----- ACN_IL1B_production4A.mdcrd (1-1250, 1) -----
> > Using first frame to determine native contacts.
> > Mask [:275] corresponds to 6 atoms.
> > Setup 0 native contacts:
> > 0% 10%
> > ----- ACN_IL1B_production4B.mdcrd (1-1250, 1) -----
> > 20%
> > ----- ACN_IL1B_production4C.mdcrd (1-1250, 1) -----
> > 30%
> > ----- ACN_IL1B_production4D.mdcrd (1-1250, 1) -----
> > 40%
> > ----- ACN_IL1B_production4E.mdcrd (1-1250, 1) -----
> > 50% 60%
> > ----- ACN_IL1B_production4F.mdcrd (1-1250, 1) -----
> > 70%
> > ----- ACN_IL1B_production4G.mdcrd (1-1250, 1) -----
> > 80%
> > ----- ACN_IL1B_production4H.mdcrd (1-1250, 1) -----
> > 90% 100% Complete.
> >
> > Read 10000 frames and processed 10000 frames.
> > TIME: Avg. throughput= 496.5572 frames / second.
> >
> > ACTION OUTPUT:
> > CONTACTS: Contacts_00002: Writing native contacts to file 'nativecontacts.dat'
> > Contacts_00002: Writing non-native contacts to file 'nativecontacts.dat'
> > Writing contacts PDB to 'contacts.pdb'
> > Writing contacts PDB to 'nn_contact.pdb'
> > TIME: Analyses took 0.0000 seconds.
> >
> > DATASETS (4 total):
> > Contacts_00002[native] "Contacts_00002[native]" (integer), size is 10000 (40.000 kB)
> > Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 10000 (40.000 kB)
> > Contacts_00002[nativemap] "Contacts_00002[nativemap]" (double matrix), size is 1 (0.068 kB)
> > Contacts_00002[nonnatmap] "Contacts_00002[nonnatmap]" (double matrix), size is 1 (0.068 kB)
> > Total data set memory usage is at least 80.136 kB
> >
> > DATAFILES (9 total):
> > contacts.out (Gnuplot File): Contacts_00002[native] Contacts_00002[nonnative]
> > nativeseries.dat (Standard Data File):
> > nn.dat (Standard Data File):
> > native.gnu (Gnuplot File): Contacts_00002[nativemap]
> > nonnative.gnu (Gnuplot File): Contacts_00002[nonnatmap]
> > nativecontacts.dat (Native Contacts)
> > contacts.pdb (Contact PDB)
> > nn_contact.pdb (Non-native Contact PDB)
> > res (Contact Res Pairs)
> > Warning: File 'nativeseries.dat' has no sets containing data.
> > Warning: File 'nn.dat' has no sets containing data.
> >
> > RUN TIMING:
> > TIME: Init : 0.0131 s ( 0.06%)
> > TIME: Trajectory Process : 20.1387 s ( 98.47%)
> > TIME: Action Post : 0.2560 s ( 1.25%)
> > TIME: Analysis : 0.0000 s ( 0.00%)
> > TIME: Data File Write : 0.0443 s ( 0.22%)
> > TIME: Other : 0.0003 s ( 0.00%)
> > TIME: Run Total 20.4523 s
> > ---------- RUN END ---------------------------------------------------
> > TIME: Total execution time: 20.7321 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.
> >
> > Which is the output file of interest in this case?
> >
> >
> > Debarati
> > Postdoctoral research fellow
> > College of Pharmacy
> > University of Michigan, USA
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: Tuesday, March 26, 2019 9:12 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] locating the single probe out of 80000 snapshots
> >
> > Hi,
> >
> > I think maybe you can do what you want with cpptraj's 'nativecontacts'
> > command. Make sure you're using the latest version. One mask would be
> > protein, the other mask would be probe molecules. Specify
> > skipnonnative to make every contact non-native, and track the
> > residences with '[savenonnative [seriesnnout <file>]' etc.
> >
> > Hope this at least begins to help,
> >
> > -Dan
> >
> > On Mon, Mar 25, 2019 at 10:58 AM Debarati DasGupta
> > <debarati_dasgupta.hotmail.com> wrote:
> > >
> > > Hi All,
> > >
> > > I think I am confused and would appreciate any help from you guys in case you have an idea as to how to go about it.
> > > I have a protein(3KFA) and I have it soaked in water+acetonitrile, water+imidazole , water+ ethanol, water+methanol, and water+ pyrimidine.
> > >
> > > Approx I have 100 probes mixed in ~3300 water molecules.
> > >
> > > Now I have mapped the regions of the protein where is favorable binding of these probes listed above.
> > >
> > > I need to calculate the distance between the mapped hotspot x,y,z coordinates (Center of mass) and the probe molecule to get a residence time for the probe in that spot.
> > > But in my case I have certain hotspots which house more than 1 probe at the same time!
> > > Now, if I want to calculate the distance between the active site (COM co ordinates) and the probe how to achieve it?
> > > Like how to label which prob (out of 100 probe molecules) have resided in my active sites?
> > >
> > > I need to calculate the distance time series in my trajectory of 80000 snapshots
> > >
> > > Thanks
> > > Debarati
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
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>
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Received on Wed Mar 27 2019 - 07:30:01 PDT
