[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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