AMBER Archive (2008)

Subject: Re: AMBER: How to build a dimer using amber

From: Reena ..... (ren.saini_at_gmail.com)
Date: Tue Jan 15 2008 - 03:31:24 CST

Hello Users,
I am satisfied with the Hex results...Best solution file was saved as a pdb
file which was then used as an input for sander....created the prmtop and
inpcrd file using leap and did minimisation and dynamics using sander.....My
problem is I want to study the other geometries also for the dimer formation
viz...
1) Parallel
2) Head to head ( N-terminal....N-terminal)
3) Head to tail ( N-terminal---C-terminal)
4) Antiparallel etc....
Is this possible with Hex?
I wanted to know if the same thing could be done using amber itself. What I
did was loaded the monomers in two different units using xleap and combined
the two units, thus forming a pdb file containing two monomers. The file I
obtained was as :

ATOM 1 1HH3 ACE 1 0.021 -0.210 3.250 1.00 0.00
ATOM 2 CH3 ACE 1 0.633 -0.904 2.674 1.00 0.00
ATOM 3 2HH3 ACE 1 1.635 -0.950 3.101 1.00 0.00
ATOM 4 3HH3 ACE 1 0.703 -0.564 1.641 1.00 0.00
ATOM 5 C ACE 1 0.006 -2.291 2.708 1.00 0.00
ATOM 6 O ACE 1 -1.049 -2.484 3.308 1.00 0.00
ATOM 7 N GLY 2 0.674 -3.264 2.084 1.00 0.00
ATOM 8 H GLY 2 1.543 -3.060 1.612 1.00 0.00
ATOM 9 CA GLY 2 0.210 -4.637 2.097 1.00 0.00
ATOM 10 2HA GLY 2 -0.878 -4.650 2.164 1.00 0.00
ATOM 11 3HA GLY 2 0.557 -5.143 1.196 1.00 0.00
ATOM 12 C GLY 2 0.792 -5.343 3.312 1.00 0.00
ATOM 13 O GLY 2 0.510 -6.516 3.547 1.00 0.00
ATOM 14 N GLY 3 1.595 -4.618 4.094 1.00 0.00
ATOM 15 H GLY 3 1.793 -3.655 3.858 1.00 0.00
ATOM 16 CA GLY 3 2.214 -5.168 5.282 1.00 0.00
ATOM 17 2HA GLY 3 2.451 -6.218 5.114 1.00 0.00
ATOM 18 3HA GLY 3 3.112 -4.595 5.516 1.00 0.00
ATOM 19 C GLY 3 1.243 -5.061 6.449 1.00 0.00
ATOM 20 O GLY 3 1.546 -5.503 7.555 1.00 0.00
ATOM 21 N GLY 4 0.062 -4.493 6.194 1.00 0.00
ATOM 22 H GLY 4 -0.143 -4.150 5.266 1.00 0.00
ATOM 23 CA GLY 4 -0.960 -4.356 7.212 1.00 0.00
ATOM 24 2HA GLY 4 - 0.485 -4.208 8.182 1.00 0.00
ATOM 25 3HA GLY 4 -1.611 -3.519 6.960 1.00 0.00
ATOM 26 C GLY 4 -1.794 -5.628 7.259 1.00 0.00
ATOM 27 O GLY 4 -2.711 -5.743 8.069 1.00 0.00
ATOM 28 N GLY 5 -1.458 -6.594 6.401 1.00 0.00
ATOM 29 H GLY 5 -0.693 -6.453 5.757 1.00 0.00
ATOM 30 CA GLY 5 -2.160 -7.861 6.359 1.00 0.00
ATOM 31 2HA GLY 5 -3.217 -7.694 6.565 1.00 0.00
ATOM 32 3HA GLY 5 -2.016 -8.320 5.381 1.00 0.00
ATOM 33 C GLY 5 -1.589 -8.783 7.427 1.00 0.00
ATOM 34 O GLY 5 - 2.059 -9.906 7.597 1.00 0.00
ATOM 35 N GLY 6 -0.592 -8.293 8.168 1.00 0.00
ATOM 36 H GLY 6 -0.243 -7.361 7.994 1.00 0.00
ATOM 37 CA GLY 6 0.020 -9.061 9.234 1.00 0.00
ATOM 38 2HA GLY 6 0.055 -10.112 8.947 1.00 0.00
ATOM 39 3HA GLY 6 1.019 -8.673 9.431 1.00 0.00
ATOM 40 C GLY 6 -0.821 -8.923 10.495 1.00 0.00
ATOM 41 O GLY 6 -0.507 -9.520 11.522 1.00 0.00
ATOM 42 N GLY 7 -1.909 -8.154 10.405 1.00 0.00
ATOM 43 H GLY 7 -2.128 -7.689 9.536 1.00 0.00
ATOM 44 CA GLY 7 - 2.810 -7.966 11.524 1.00 0.00
ATOM 45 2HA GLY 7 -2.238 -7.968 12.452 1.00 0.00
ATOM 46 3HA GLY 7 -3.350 -7.028 11.397 1.00 0.00
ATOM 47 C GLY 7 -3.811 -9.111 11.558 1.00 0.00
ATOM 48 O GLY 7 -4.658 -9.172 12.446 1.00 0.00
ATOM 49 N GLY 8 -3.695 -10.034 10.601 1.00 0.00
ATOM 50 H GLY 8 -2.979 -9.942 9.894 1.00 0.00
ATOM 51 CA GLY 8 -4.571 -11.186 10.536 1.00 0.00
ATOM 52 2HA GLY 8 -5.572 -10.897 10.857 1.00 0.00
ATOM 53 3HA GLY 8 -4.581 -11.575 9.518 1.00 0.00
ATOM 54 C GLY 8 - 4.046 -12.266 11.472 1.00 0.00
ATOM 55 O GLY 8 -4.653 -13.326 11.604 1.00 0.00
ATOM 56 N GLY 9 -2.929 -11.980 12.144 1.00 0.00
ATOM 57 H GLY 9 -2.470 -11.091 12.005 1.00 0.00
ATOM 58 CA GLY 9 -2.341 -12.909 13.087 1.00 0.00
ATOM 59 2HA GLY 9 -2.509 -13.929 12.742 1.00 0.00
ATOM 60 3HA GLY 9 -1.276 -12.697 13.186 1.00 0.00
ATOM 61 C GLY 9 -3.005 -12.731 14.445 1.00 0.00
ATOM 62 O GLY 9 -2.662 -13.421 15.402 1.00 0.00
ATOM 63 N GLY 10 -3.967 -11.808 14.522 1.00 0.00
ATOM 64 H GLY 10 - 4.213 -11.265 13.707 1.00 0.00
ATOM 65 CA GLY 10 -4.677 -11.544 15.757 1.00 0.00
ATOM 66 2HA GLY 10 -3.986 -11.631 16.595 1.00 0.00
ATOM 67 3HA GLY 10 -5.117 -10.548 15.714 1.00 0.00
ATOM 68 C GLY 10 -5.789 -12.570 15.930 1.00 0.00
ATOM 69 O GLY 10 -6.511 -12.544 16.924 1.00 0.00
ATOM 70 N GLY 11 -5.906 -13.493 14.972 1.00 0.00
ATOM 71 H GLY 11 -5.284 -13.480 14.177 1.00 0.00
ATOM 72 CA GLY 11 -6.899 -14.547 15.045 1.00 0.00
ATOM 73 2HA GLY 11 -7.791 -14.170 15.544 1.00 0.00
ATOM 74 3HA GLY 11 - 7.129 -14.893 14.037 1.00 0.00
ATOM 75 C GLY 11 -6.335 -15.710 15.847 1.00 0.00
ATOM 76 O GLY 11 -7.040 -16.680 16.120 1.00 0.00
ATOM 77 N GLY 12 -5.069 -15.594 16.255 1.00 0.00
ATOM 78 H GLY 12 -4.534 -14.773 16.010 1.00 0.00
ATOM 79 CA GLY 12 -4.421 -16.615 17.052 1.00 0.00
ATOM 80 2HA GLY 12 -4.841 -17.589 16.803 1.00 0.00
ATOM 81 3HA GLY 12 -3.347 -16.590 16.862 1.00 0.00
ATOM 82 C GLY 12 -4.664 -16.331 18.527 1.00 0.00
ATOM 83 O GLY 12 -4.161 -17.049 19.389 1.00 0.00
ATOM 84 N GLY 13 - 5.420 -15.270 18.818 1.00 0.00
ATOM 85 H GLY 13 -5.804 -14.703 18.075 1.00 0.00
ATOM 86 CA GLY 13 -5.685 -14.876 20.187 1.00 0.00
ATOM 87 2HA GLY 13 -4.794 -15.053 20.789 1.00 0.00
ATOM 88 3HA GLY 13 -5.973 -13.825 20.209 1.00 0.00
ATOM 89 C GLY 13 -6.827 -15.715 20.744 1.00 0.00
ATOM 90 O GLY 13 -7.140 -15.632 21.929 1.00 0.00
ATOM 91 N NME 14 -7.399 -16.577 19.901 1.00 0.00
ATOM 92 H NME 14 -7.097 -16.616 18.938 1.00 0.00
ATOM 93 CH3 NME 14 -8.436 -17.497 20.325 1.00 0.00
ATOM 94 1HH3 NME 14 - 9.402 -17.156 19.954 1.00 0.00
ATOM 95 2HH3 NME 14 -8.224 -18.489 19.927 1.00 0.00
ATOM 96 3HH3 NME 14 -8.461 -17.541 21.414 1.00 0.00
TER
ATOM 97 1HH3 ACE 15 0.779 -1.252 4.244 1.00 0.00
ATOM 98 CH3 ACE 15 1.401 -2.031 3.804 1.00 0.00
ATOM 99 2HH3 ACE 15 2.313 -2.148 4.390 1.00 0.00
ATOM 100 3HH3 ACE 15 1.668 -1.755 2.784 1.00 0.00
ATOM 101 C ACE 15 0.639 -3.348 3.788 1.00 0.00
ATOM 102 O ACE 15 -0.492 -3.418 4.263 1.00 0.00
ATOM 103 N GLY 16 1.269 -4.398 3.257 1.00 0.00
ATOM 104 H GLY 16 2.200 -4.291 2.881 1.00 0.00
ATOM 105 CA GLY 16 0.665 -5.715 3.215 1.00 0.00
ATOM 106 2HA GLY 16 -0.420 -5.613 3.167 1.00 0.00
ATOM 107 3HA GLY 16 1.048 -6.259 2.353 1.00 0.00
ATOM 108 C GLY 16 1.037 -6.476 4.480 1.00 0.00
ATOM 109 O GLY 16 0.621 -7.617 4.667 1.00 0.00
ATOM 110 N GLY 17 1.816 -5.833 5.353 1.00 0.00
ATOM 111 H GLY 17 2.133 -4.896 5.148 1.00 0.00
ATOM 112 CA GLY 17 2.243 -6.440 6.597 1.00 0.00
ATOM 113 2HA GLY 17 2.391 -7.509 6.445 1.00 0.00
ATOM 114 3HA GLY 17 3.162 -5.959 6.932 1.00 0.00
ATOM 115 C GLY 17 1.167 -6.237 7.654 1.00 0.00
ATOM 116 O GLY 17 1.298 -6.718 8.778 1.00 0.00
ATOM 117 N GLY 18 0.084 -5.551 7.281 1.00 0.00
ATOM 118 H GLY 18 0.024 -5.174 6.346 1.00 0.00
ATOM 119 CA GLY 18 -1.021 -5.304 8.185 1.00 0.00
ATOM 120 2HA GLY 18 -0.633 -5.173 9.196 1.00 0.00
ATOM 121 3HA GLY 18 -1.565 -4.420 7.854 1.00 0.00
ATOM 122 C GLY 18 -1.966 -6.497 8.171 1.00 0.00
ATOM 123 O GLY 18 -2.971 -6.505 8.878 1.00 0.00
ATOM 124 N GLY 19 -1.633 -7.514 7.373 1.00 0.00
ATOM 125 H GLY 19 -0.796 -7.461 6.811 1.00 0.00
ATOM 126 CA GLY 19 -2.439 -8.715 7.284 1.00 0.00
ATOM 127 2HA GLY 19 - 3.491 -8.456 7.402 1.00 0.00
ATOM 128 3HA GLY 19 -2.259 -9.195 6.322 1.00 0.00
ATOM 129 C GLY 19 -2.041 -9.672 8.398 1.00 0.00
ATOM 130 O GLY 19 -2.598 -10.761 8.515 1.00 0.00
ATOM 131 N GLY 20 -1.083 -9.253 9.229 1.00 0.00
ATOM 132 H GLY 20 -0.655 -8.349 9.088 1.00 0.00
ATOM 133 CA GLY 20 -0.612 -10.062 10.336 1.00 0.00
ATOM 134 2HA GLY 20 -0.600 -11.110 10.040 1.00 0.00
ATOM 135 3HA GLY 20 0.382 -9.725 10.627 1.00 0.00
ATOM 136 C GLY 20 -1.553 -9.897 11.521 1.00 0.00
ATOM 137 O GLY 20 - 1.335 -10.489 12.576 1.00 0.00
ATOM 138 N GLY 21 -2.609 -9.101 11.341 1.00 0.00
ATOM 139 H GLY 21 -2.745 -8.634 10.455 1.00 0.00
ATOM 140 CA GLY 21 -3.582 -8.869 12.389 1.00 0.00
ATOM 141 2HA GLY 21 -3.073 -8.842 13.353 1.00 0.00
ATOM 142 3HA GLY 21 -4.102 -7.931 12.195 1.00 0.00
ATOM 143 C GLY 21 -4.598 -10.003 12.400 1.00 0.00
ATOM 144 O GLY 21 -5.503 -10.018 13.231 1.00 0.00
ATOM 145 N GLY 22 -4.438 -10.963 11.486 1.00 0.00
ATOM 146 H GLY 22 -3.677 -10.908 10.824 1.00 0.00
ATOM 147 CA GLY 22 - 5.336 -12.098 11.400 1.00 0.00
ATOM 148 2HA GLY 22 -6.342 -11.782 11.677 1.00 0.00
ATOM 149 3HA GLY 22 -5.316 -12.498 10.386 1.00 0.00
ATOM 150 C GLY 22 -4.876 -13.180 12.366 1.00 0.00
ATOM 151 O GLY 22 -5.488 -14.243 12.448 1.00 0.00
ATOM 152 N GLY 23 -3.799 -12.904 13.103 1.00 0.00
ATOM 153 H GLY 23 -3.332 -12.015 12.999 1.00 0.00
ATOM 154 CA GLY 23 -3.260 -13.847 14.063 1.00 0.00
ATOM 155 2HA GLY 23 -3.419 -14.863 13.701 1.00 0.00
ATOM 156 3HA GLY 23 -2.199 -13.643 14.212 1.00 0.00
ATOM 157 C GLY 23 - 3.980 -13.679 15.393 1.00 0.00
ATOM 158 O GLY 23 -3.665 -14.365 16.363 1.00 0.00
ATOM 159 N GLY 24 -4.946 -12.759 15.440 1.00 0.00
ATOM 160 H GLY 24 -5.165 -12.213 14.619 1.00 0.00
ATOM 161 CA GLY 24 -5.683 -12.486 16.658 1.00 0.00
ATOM 162 2HA GLY 24 -5.006 -12.550 17.509 1.00 0.00
ATOM 163 3HA GLY 24 -6.134 -11.496 16.592 1.00 0.00
ATOM 164 C GLY 24 -6.785 -13.524 16.831 1.00 0.00
ATOM 165 O GLY 24 -7.535 -13.476 17.804 1.00 0.00
ATOM 166 N GLY 25 -6.869 -14.474 15.898 1.00 0.00
ATOM 167 H GLY 25 - 6.228 -14.477 15.118 1.00 0.00
ATOM 168 CA GLY 25 -7.858 -15.531 15.971 1.00 0.00
ATOM 169 2HA GLY 25 -8.760 -15.151 16.452 1.00 0.00
ATOM 170 3HA GLY 25 -8.071 -15.894 14.966 1.00 0.00
ATOM 171 C GLY 25 -7.304 -16.683 16.799 1.00 0.00
ATOM 172 O GLY 25 -8.007 -17.656 17.062 1.00 0.00
ATOM 173 N GLY 26 -6.046 -16.558 17.227 1.00 0.00
ATOM 174 H GLY 26 -5.511 -15.736 16.986 1.00 0.00
ATOM 175 CA GLY 26 -5.402 -17.575 18.032 1.00 0.00
ATOM 176 2HA GLY 26 -5.814 -18.552 17.779 1.00 0.00
ATOM 177 3HA GLY 26 - 4.327 -17.545 17.856 1.00 0.00
ATOM 178 C GLY 26 -5.663 -17.295 19.505 1.00 0.00
ATOM 179 O GLY 26 -5.160 -18.007 20.372 1.00 0.00
ATOM 180 N GLY 27 -6.430 -16.240 19.790 1.00 0.00
ATOM 181 H GLY 27 -6.811 -15.674 19.045 1.00 0.00
ATOM 182 CA GLY 27 -6.702 -15.844 21.158 1.00 0.00
ATOM 183 2HA GLY 27 -5.809 -16.009 21.761 1.00 0.00
ATOM 184 3HA GLY 27 -7.000 -14.796 21.176 1.00 0.00
ATOM 185 C GLY 27 -7.834 -16.693 21.718 1.00 0.00
ATOM 186 O GLY 27 -8.149 -16.607 22.902 1.00 0.00
ATOM 187 N NME 28 - 8.397 -17.567 20.879 1.00 0.00
ATOM 188 H NME 28 -8.093 -17.608 19.917 1.00 0.00
ATOM 189 CH3 NME 28 -9.424 -18.494 21.309 1.00 0.00
ATOM 190 1HH3 NME 28 -10.395 -18.160 20.941 1.00 0.00
ATOM 191 2HH3 NME 28 -9.206 -19.485 20.910 1.00 0.00
ATOM 192 3HH3 NME 28 -9.443 -18.538 22.398 1.00 0.00
TER
END
But the problem I think is, since the two strands are two close.......when
the minimisation /dynamics is performed the change in conformation will not
be much as the two monomers wil stabilise in each others vicinity....to me
it seems a biased result. I want to see if the two monomers come together in
a system how wil they interact, and what change wil the conformation of the
individuals undergo in such a system. Also, with combine command the
monomers come in a parallel fashion....how to go about other geometries.
I want to study the highermers viz, trimer, tetramer....etc so I need to
know a way wherein I can put the various combinations of the monomers n the
highermers in the system to study the small peptide molecules

regards
Reena

On Jan 15, 2008 1:21 PM, David A. Case <case_at_scripps.edu> wrote:

> On Tue, Jan 15, 2008, Reena ..... wrote:
> >
> > I have tried placing the "ter" card and the combine command in xleap.
>
> You need to be a *lot* more specific in what you did. Please give the
> exact
> commands, what try to say precisely what was wrong with the result.
>
> > I have also used Hex, wherein the resulting file had two monomers in
> > antiparallel geometry as the most stable structure. This file was used
> as
> > input structure for the minimisation n dynamics run in Amber.
>
> Sounds fine to me. Are you trying to say that you are satisfied or
> dis-satisfied with using this Hex structure?
>
> Again, please tell us exactly what you did, in as much detail as possible.
>
> Don't just say "the resulting file...": what kind of file is it? how
> exactly
> did you input this into Amber?
>
> I'm not trying to be critical here, just trying to point out what sort of
> information you will need to provide if anyone is going to be able to
> help.
>
> ...dac
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