[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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