[gmx-users] bad bond in polymer

nicegromacs nicegromacs at live.cl
Fri Aug 14 20:18:52 CEST 2009


Hi Justin,

the pdb file:

HETATM    1  CAA DRG     1      83.043  46.127  36.820
HETATM    2  CAB DRG     1      82.411  45.765  35.421
HETATM    3  CAC DRG     1      81.495  46.822  34.598
HETATM    4  CAD DRG     1      80.621  46.369  33.071
HETATM    5  CAE DRG     1      79.305  47.302  32.172
HETATM    6  CAF DRG     1      77.939  46.749  31.124
HETATM    7  CAG DRG     1      76.264  47.439  30.612
HETATM    8  CAH DRG     1      74.636  46.805  29.962
HETATM    9  CAI DRG     1      72.805  47.674  30.179
HETATM   10  CAJ DRG     1      73.794  48.838  31.123
HETATM   11  OAK DRG     1      74.815  49.342  30.292
HETATM   12  OAL DRG     1      74.592  48.143  32.194
HETATM   13  CAM DRG     1      71.093  47.685  29.486
HETATM   14  CAN DRG     1      71.598  47.212  28.208
HETATM   15  OAO DRG     1      72.440  48.255  27.735
HETATM   16  OAP DRG     1      72.374  46.050  28.399
HETATM   17  CAA DRG     1      72.093  46.197  36.714
HETATM   18  CAB DRG     1      71.418  45.759  35.400
HETATM   19  CAC DRG     1      71.084  46.901  34.417
HETATM   20  CAD DRG     1      70.620  46.251  33.139
HETATM   21  CAE DRG     1      70.650  47.255  32.000
HETATM   22  CAF DRG     1      69.655  46.512  30.955
HETATM   23  CAG DRG     1      69.081  47.504  29.843
HETATM   24  CAH DRG     1      67.208  47.518  29.256
HETATM   25  CAI DRG     1      65.298  47.601  29.691
HETATM   26  CAJ DRG     1      65.629  48.362  30.827
HETATM   27  OAK DRG     1      65.140  49.590  30.429
HETATM   28  OAL DRG     1      64.837  47.815  31.709
HETATM   29  CAM DRG     1      63.041  47.557  29.333
HETATM   30  CAN DRG     1      62.808  47.023  27.931
HETATM   31  OAO DRG     1      63.130  48.142  27.185
HETATM   32  OAP DRG     1      63.560  45.894  27.706
HETATM   33  CAA DRG     1      61.174  46.188  36.668
HETATM   34  CAB DRG     1      60.510  45.777  35.344
HETATM   35  CAC DRG     1      60.221  46.928  34.352
HETATM   36  CAD DRG     1      59.724  46.337  32.998
HETATM   37  CAE DRG     1      60.252  47.307  31.985
HETATM   38  CAF DRG     1      61.089  46.606  30.881
HETATM   39  CAG DRG     1      60.868  47.564  29.740
HETATM   40  CAH DRG     1      58.621  47.652  29.253
HETATM   41  CAI DRG     1      56.328  47.703  29.755
HETATM   42  CAJ DRG     1      55.914  48.516  30.963
HETATM   43  OAK DRG     1      55.050  49.545  30.403
HETATM   44  OAL DRG     1      54.945  47.724  31.565
HETATM   45  CAM DRG     1      54.420  47.478  29.367
HETATM   46  CAN DRG     1      53.587  47.142  27.983
HETATM   47  OAO DRG     1      52.713  48.009  27.325
HETATM   48  OAP DRG     1      53.396  45.805  27.517
HETATM   49  CAA DRG     1      50.257  46.173  36.646
HETATM   50  CAB DRG     1      49.673  45.778  35.270
HETATM   51  CAC DRG     1      49.360  46.939  34.273
HETATM   52  CAD DRG     1      49.270  46.480  32.735
HETATM   53  CAE DRG     1      50.289  47.086  31.602
HETATM   54  CAF DRG     1      51.813  46.713  31.234
HETATM   55  CAG DRG     1      52.487  47.720  29.966
HETATM   56  CAH DRG     1      50.870  47.989  29.178
HETATM   57  CAI DRG     1      48.982  47.816  29.191
HETATM   58  CAJ DRG     1      47.901  48.319  30.192
HETATM   59  OAK DRG     1      47.004  49.132  29.503
HETATM   60  OAL DRG     1      46.963  47.171  30.588
HETATM   61  CAM DRG     1      47.752  46.922  28.157
HETATM   62  CAN DRG     1      46.372  47.149  27.020
HETATM   63  OAO DRG     1      45.018  47.950  26.877
HETATM   64  OAP DRG     1      46.019  46.082  26.137


--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Friday, August 14, 2009 12:14 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer

>
>
> nicegromacs wrote:
>> I follow some of the step of 
>> http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I 
>> omitted the change in the .hdb file because I don't have explicit 
>> hydrogens). Well, I build a polymer with 3 units. The head (H), one 
>> repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives ok, 
>> but when I add one more repetitive unit (H-R-R-T) I get the following 
>> error:
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: ../../../../src/kernel/pgutil.c, line: 87
>> Fatal error:
>> Atom CAM not found in residue 1083339441 while adding improper
>>
>> -------------------------------------------------------
>>
>
> It looks like pdb2gmx is finding some kind of undefined residue.  Can you 
> post the .pdb file?
>
> -Justin
>
>> "Stop Drinking My Beer !" (The Amps)
>>
>>
>>>
>>>
>>> nicegromacs wrote:
>>>
>>>>   CAG -CAM
>>>
>>> Defining a bond to a previous residue will certainly fail for at least 
>>> one terminus of your polymer chain.  You may find this post useful:
>>>
>>> http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
>>>
>>> If things still aren't working, please post the structure file, as well, 
>>> and identify the bond that is being formed that shouldn't.
>>>
>>> -Justin
>>>
>>> -- 
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> _______________________________________________
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>>
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
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