[gmx-users] Problem in making index.ndx and disres.itp
Justin Lemkul
jalemkul at vt.edu
Mon Mar 16 12:29:01 CET 2015
On 3/16/15 4:36 AM, Tushar Ranjan Moharana wrote:
> 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
Why don't you think it's correct?
-Justin
> 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
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> *; 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*
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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