I'd like to create 1 xplor file that shows when either C3N or IPA occupies
a site so that I can easily see which sites are most frequently occupied by
multiple solvents. I can sum maps in pymol, and was hoping that I'd be
able to do something similar within cpptraj. Am I correct in saying that
this is not possible within cpptraj?
On Tue, Jul 26, 2016 at 3:11 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Tue, Jul 26, 2016 at 11:17 AM, Sarah Graham <sarahgra.umich.edu> wrote:
> > I'm running MD simulations with mixed solvent. I have one set of
> > simulations with acetonitrile and water and another set with isopropyl
> > alcohol and water (with the same protein in both). I'd like to combine
> the
> > trajectories in cpptraj and use the grid command to count up when either
> > acetonitrile or isopropyl alcohol is at a site. I'm using cpptraj in
> > ambertools14. I can successfully read in both trajectories and align
> them,
> > and then use the grid command on one solvent or the other, but the grid
> > command seems to only recognize one of the co-solvents when I try to use
> > the grid command on both. Is it possible to calculate this in cpptraj?
>
> You are reading in two trajectories, each corresponding to a different
> topology. One topology contains residues named C3N, while the other
> topology contains IPA, right? If that is the case, then when cpptraj
> is processing the trajectory containing C3N, the mask ":C3N,IPA" can
> *only* select the C3N residues (according to cpptraj this totals 1578
> atoms or 268 acetonitrile residues). Similarly, when cpptraj is
> processing the trajectory containing IPA, the mask ":C3N,IPA" can
> *only* select the IPA residues (according to cpptraj this is 2184
> atoms or 182 isopropyl alcohol residues). So based on the output you
> provided it seems like everything is being calculated the way you
> want. However, if what you want to see is whether these residues are
> occupying the same site, your best bet may be to just create separate
> grids for each residue (i.e. each trajectory) and view them overlaid
> on top of each other. The reason is that with the combined grid you
> have no way of telling what density corresponds to what residue, and
> the larger IPA residue will obscure any C3N density anyway.
>
> Hope this helps,
>
> -Dan
>
> >
> > Here is the input file I'm using:
> >
> >
> > parm /archive/sarahgra/1DG8/ACN_1DG8/run_1/ACN_1DG8.prmtop [ACN_prmtop]
> > trajin /archive/sarahgra/1DG8/ACN_1DG8/run_1/New4E_production.1.crd.bz2
> > parm [ACN_prmtop]
> >
> > parm /archive/sarahgra/1DG8/IPA_1DG8/run_1/IPA_1DG8.prmtop [IPA_prmtop]
> > trajin /archive/sarahgra/1DG8/IPA_1DG8/run_1/New4E_production.1.crd.bz2
> > parm [IPA_prmtop]
> >
> > autoimage
> > reference /archive/sarahgra/1DG8/ACN_1DG8/run_1/ACN_1DG8.pdb parm
> > [ACN_prmtop]
> >
> > strip :Cl-,Na+
> > rms reference out rmsd_core.txt :1-161.CA
> >
> > #Write out grid count of probe occupancy
> > #grid ACN_1DG8_last-10ns.xplor 200 0.5 200 0.5 200 0.5 :C3N (This works
> > fine)
> > #grid IPA_1DG8_last-10ns.xplor 200 0.5 200 0.5 200 0.5 :IPA (This works
> > fine)
> > grid ACN_IPA_1DG8_last-10ns.xplor 200 0.5 200 0.5 200 0.5 :C3N,IPA (This
> > only gives me results for C3N or IPA at a time, not both)
> >
> >
> > *Part of output file:*
> > Warning: after the RMS-fit is performed.
> > 3: [grid ACN_IPA_1DG8_last-10ns.xplor 200 0.5 200 0.5 200 0.5 :C3N,IPA]
> > Mask [:C3N,IPA] corresponds to 1578 atoms.
> > ----- New4E_production.1.crd.bz2 (1-EOF, 1) -----
> > 0 ++++++
> > Progress: '+' = 200 iterations.
> > .....................................................
> > ACTION SETUP FOR PARM '[IPA_prmtop]' (4 actions):
> > 0: [autoimage]
> > Anchor molecule is 1
> > The following molecules are fixed to anchor: 2 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
> > 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147
> 148
> > 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166
> 167
> > 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185
> 186
> > 187 188 189
> > 14668 molecules are mobile.
> > 1: [strip :Cl-,Na+]
> > Stripping 5 atoms.
> > Stripped parm:
> > '/archive/sarahgra/1DG8/IPA_1DG8/run_1/IPA_1DG8.prmtop', 48723 atoms,
> 15007
> > res, box: Orthogonal, 14847 mol, 14663 solvent
> > 2: [rms reference out rmsd_core.txt :1-161.CA]
> > Target mask: [:1-161.CA](159)
> > Warning: Coordinates are being rotated and box coordinates are present.
> > Warning: Unit cell vectors are NOT rotated; imaging will not be possible
> > Warning: after the RMS-fit is performed.
> > 3: [grid ACN_IPA_1DG8_last-10ns.xplor 200 0.5 200 0.5 200 0.5 :C3N,IPA]
> > Mask [:C3N,IPA] corresponds to 2184 atoms.
> > ----- New4E_production.1.crd.bz2 (1-EOF, 1) -----
> > 0 ++++++
> > Read 2500 frames and processed 2500 frames.
> > TIME: Trajectory processing: 280.0873 s
> > TIME: Avg. throughput= 8.9258 frames / second.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Tue Jul 26 2016 - 13:30:03 PDT
