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.
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--
-------------------------
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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Received on Tue Jul 26 2016 - 12:30:02 PDT
