[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
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *; 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

==================================================


More information about the gromacs.org_gmx-users mailing list