Hi,
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?
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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Received on Tue Jul 26 2016 - 10:30:02 PDT
