[gmx-users] Problem in making index.ndx and disres.itp
Tushar Ranjan Moharana
tusharranjanmoharana at gmail.com
Mon Mar 16 09:36:04 CET 2015
Hi everyone,
I wanted to run a distance restricted MD. Since I have many atoms I can't
do it manually with a text editor. For that I choose the line corresponding
the atom from .pdb file to another text file and rename them as disres.pdb.
Then I run the following command to generate disres.itp
*gmx genrestr -f disres.pdb -disre -o disres.itp*
I got the following out put Which I don't think correct. Please rectify my
mistakes
My disres.pdb file
ATOM 936 CG ASP 61 -36.433 1.944 57.629 0.7994
1.700 C
ATOM 937 OD1 ASP 61 -37.626 1.784 58.005 -0.8014
1.500 O
ATOM 938 OD2 ASP 61 -35.856 3.065 57.600 -0.8014
1.500 O
ATOM 1212 CD2 HIS 81 -41.384 3.133 58.251 -0.1141
1.700 C
ATOM 1208 CE1 HIS 81 -41.090 2.008 60.045 -0.0170
1.700 C
ATOM 1211 HE2 HIS 81 -39.455 3.044 59.220 0.3911
1.300 H
ATOM 1295 CD2 HIS 87 -38.577 6.571 57.666 0.1292
1.700 C
ATOM 1292 CE1 HIS 87 -39.069 5.316 56.005 0.2057
1.700 C
ATOM 1294 NE2 HIS 87 -39.012 5.303 57.324 -0.5727
1.550 N
ATOM 3657 CG ASP 238 -37.842 3.869 61.472 0.7994
1.700 C
ATOM 3658 OD1 ASP 238 -37.982 2.630 61.652 -0.8014
1.500 O
ATOM 3659 OD2 ASP 238 -37.595 4.399 60.357 -0.8014
1.500 O
END
My disres.itp file
*; distance restraints for SideChain of [ distance_restraints ]; i j
? label funct lo up1 up2 weight 1 2
1 0 1 0.026104 0.226104 1.2261 1 1 3
1 1 1 0.0261116 0.226112 1.22611 1 1 4
1 2 1 0.412962 0.612962 1.61296 1 1 5
1 3 1 0.424679 0.624679 1.62468 1 1 6
1 4 1 0.2588 0.4588 1.4588 1 1 7
1 5 1 0.409973 0.609973 1.60997 1 1 8
1 6 1 0.35778 0.55778 1.55778 1 1 9
1 7 1 0.324584 0.524584 1.52458 1 1 10
1 8 1 0.352323 0.552323 1.55232 1 1 11
1 9 1 0.336515 0.536515 1.53652 1 1 12
1 10 1 0.284958 0.484958 1.48496 1 2 3
1 11 1 0.122214 0.322214 1.32221 1 2 4
1 12 1 0.300036 0.500036 1.50004 1 2 5
1 13 1 0.30263 0.50263 1.50263 1 2 6
1 14 1 0.153161 0.353161 1.35316 1 2 7
1 15 1 0.389231 0.589231 1.58923 1 2 8
1 16 1 0.330781 0.530781 1.53078 1 2 9
1 17 1 0.284293 0.484293 1.48429 1 2 10
1 18 1 0.305142 0.505142 1.50514 1 2 11
1 19 1 0.276073 0.476073 1.47607 1 2 12
1 20 1 0.251726 0.451726 1.45173 1 3 4
1 21 1 0.456662 0.656662 1.65666 1 3 5
1 22 1 0.487282 0.687282 1.68728 1 3 6
1 23 1 0.294685 0.494685 1.49469 1 3 7
1 24 1 0.34385 0.54385 1.54385 1 3 8
1 25 1 0.32349 0.52349 1.52349 1 3 9
1 26 1 0.287881 0.487881 1.48788 1 3 10
1 27 1 0.342527 0.542527 1.54253 1 3 11
1 28 1 0.35965 0.55965 1.55965 1 3 12
1 29 1 0.252203 0.452203 1.4522 1 4 5
1 30 1 0.113787 0.313787 1.31379 1 4 6
1 31 1 0.116054 0.316054 1.31605 1 4 7
1 32 1 0.347675 0.547675 1.54768 1 4 8
1 33 1 0.289477 0.489477 1.48948 1 4 9
1 34 1 0.234584 0.434584 1.43458 1 4 10
1 35 1 0.384379 0.584379 1.58438 1 4 11
1 36 1 0.383668 0.583668 1.58367 1 4 12
1 37 1 0.351603 0.551603 1.5516 1 5 6
1 38 1 0.110408 0.310408 1.31041 1 5 7
1 39 1 0.472676 0.672676 1.67268 1 5 8
1 40 1 0.459901 0.659901 1.6599 1 5 9
1 41 1 0.375173 0.575173 1.57517 1 5 10
1 42 1 0.300614 0.500614 1.50061 1 5 11
1 43 1 0.255373 0.455373 1.45537 1 5 12
1 44 1 0.324609 0.524609 1.52461 1 6 7
1 45 1 0.295291 0.495291 1.49529 1 6 8
1 46 1 0.295565 0.495565 1.49557 1 6 9
1 47 1 0.198231 0.398231 1.39823 1 6 10
1 48 1 0.189031 0.389031 1.38903 1 6 11
1 49 1 0.187328 0.387328 1.38733 1 6 12
1 50 1 0.156679 0.356679 1.35668 1 7 8
1 51 1 0.113916 0.313916 1.31392 1 7 9
1 52 1 0.0383479 0.238348 1.23835 1 7 10
1 53 1 0.372511 0.572511 1.57251 1 7 11
1 54 1 0.463682 0.663682 1.66368 1 7 12
1 55 1 0.259491 0.459491 1.45949 1 8 9
1 56 1 0.0320293 0.232029 1.23203 1 8 10
1 57 1 0.478683 0.678683 1.67868 1 8 11
1 58 1 0.534703 0.734703 1.7347 1 8 12
1 59 1 0.368545 0.568545 1.56855 1 9 10
1 60 1 0.354216 0.554216 1.55422 1 9 11
1 61 1 0.419013 0.619013 1.61901 1 9 12
1 62 1 0.246759 0.446759 1.44676 1 10 11
1 63 1 0.025981 0.225981 1.22598 1 10 12
1 64 1 0.0259023 0.225902 1.2259 1 11 12
1 65 1 0.122624 0.322624 1.32262 1*
--
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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