[gmx-users] bad bond in polymer

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 14 21:30:51 CEST 2009



nicegromacs wrote:
> Hi Justin,
> Ok, I have done some arrangements to the .rtp file (whit the same pdb 
> file DR0-DRG-DRG-DR1) but I still have the same error.
> 

Using these .rtp entries with the .pdb file you posted (after adjusting the 
residue names) works for me, using version 4.0.5.  Do you have problems with 
other standard structures?  It was weird that pdb2gmx was spitting out infinite 
residue numbers.  Does your installation pass the test set?

-Justin

> the rtp file is:
> [ DRG ]   ;
> [ atoms ]
>   CAA  CH3    0.000     1
>   CAB  CH2    0.000     1
>   CAC  CH2    0.000     1
>   CAD  CH2    0.000     1
>   CAE  CH2    0.000     2
>   CAF  CH2    0.000     2
>   CAG  CH1    0.000     3
>   CAH  CH2    0.041     4
>   CAI  CH1    0.107     4
>   CAJ    C    0.352     4
>   OAK   OM   -0.750     4
>   OAL   OM   -0.750     4
>   CAM  CH2    0.044     5
>   CAN    C    0.373     5
>   OAO   OM   -0.709     5
>   OAP   OM   -0.708     5
> [ bonds ]
>   CAM -CAG
>   CAA  CAB
>   CAB  CAC
>   CAC  CAD
>   CAD  CAE
>   CAE  CAF
>   CAF  CAG
>   CAG  CAH
>   CAH  CAI
>   CAI  CAJ
>   CAI  CAM
>   CAJ  OAK
>   CAJ  OAL
>   CAM  CAN
>   CAN  OAO
>   CAN  OAP
>   CAG +CAM
> [ impropers ]
>   CAG  CAF -CAM  CAH
>  -CAM -CAN -CAI  CAG
>   CAJ  CAI  OAL  OAK
>   CAN  CAM  OAP  OAO
>   CAI  CAH  CAJ  CAM
> 
> ;  head of the polymer
> 
> [ DR1 ]
> [ atoms ]
>   CAA  CH3    0.000     1
>   CAB  CH2    0.000     1
>   CAC  CH2    0.000     1
>   CAD  CH2    0.000     1
>   CAE  CH2    0.000     2
>   CAF  CH2    0.000     2
>   CAG  CH1    0.000     3
>   CAH  CH2    0.041     4
>   CAI  CH1    0.107     4
>   CAJ    C    0.352     4
>   OAK   OM   -0.750     4
>   OAL   OM   -0.750     4
>   CAM  CH2    0.044     5
>   CAN    C    0.373     5
>   OAO   OM   -0.709     5
>   OAP   OM   -0.708     5
> [ bonds ]
>   CAA  CAB
>   CAB  CAC
>   CAC  CAD
>   CAD  CAE
>   CAE  CAF
>   CAF  CAG
>   CAG  CAH
>   CAH  CAI
>   CAI  CAJ
>   CAI  CAM
>   CAJ  OAK
>   CAJ  OAL
>   CAM  CAN
>   CAN  OAO
>   CAN  OAP
>   CAG +CAM
> [ impropers ]
>   CAG  CAF +CAM  CAH
>  +CAM +CAN +CAI  CAG
>   CAJ  CAI  OAL  OAK
>   CAN  CAM  OAP  OAO
>   CAI  CAH  CAJ  CAM
> 
> ; the tail of the polymer
> [ DR2 ]
> [ atoms ]
>   CAA  CH3    0.000     1
>   CAB  CH2    0.000     1
>   CAC  CH2    0.000     1
>   CAD  CH2    0.000     1
>   CAE  CH2    0.000     2
>   CAF  CH2    0.000     2
>   CAG  CH1    0.000     3
>   CAH  CH2    0.041     4
>   CAI  CH1    0.107     4
>   CAJ    C    0.352     4
>   OAK   OM   -0.750     4
>   OAL   OM   -0.750     4
>   CAM  CH2    0.044     5
>   CAN    C    0.373     5
>   OAO   OM   -0.709     5
>   OAP   OM   -0.708     5
> [ bonds ]
>   CAM -CAG
>   CAA  CAB
>   CAB  CAC
>   CAC  CAD
>   CAD  CAE
>   CAE  CAF
>   CAF  CAG
>   CAG  CAH
>   CAH  CAI
>   CAI  CAJ
>   CAI  CAM
>   CAJ  OAK
>   CAJ  OAL
>   CAM  CAN
>   CAN  OAO
>   CAN  OAP
> [ impropers ]
>   CAG  CAF -CAM  CAH
>  -CAM -CAN -CAI  CAG
>   CAJ  CAI  OAL  OAK
>   CAN  CAM  OAP  OAO
>   CAI  CAH  CAJ  CAM
> 
> --------------------------------------------------
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Sent: Friday, August 14, 2009 2:46 PM
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] bad bond in polymer
> 
>>
>> The problem is in how you handle impropers.  From your previous post, 
>> your [DRG] entry had the following:
>>
>> [ impropers ]
>>   CAG  CAF -CAM  C
>>  -CAM -CAN -CAI  C
>>   CAJ  CAI  OAL  O
>>   CAN  CAM  OAP  O
>>   CAI  CAH  CAJ  C
>>
>> The last column needs to correspond to an actual atom name; there may 
>> also be issues with atom naming, since that previous post also had 
>> different atom names for DR0, DRG, and DR1 residues.  In the attached 
>> .pdb file, you appear to have uniform naming between all of the residues.
>>
>> Be careful which files you are using; it looks like you have made 
>> multiple attempts.  If things still aren't working out, please post:
>>
>> 1. The error message you are getting.
>> 2. The .pdb file.
>> 3. The current .rtp entries.
>>
>> -Justin
>>
>> nicegromacs wrote:
>>> Hi Justin,
>>>
>>> ups!! I am sorry this is the exact .pdb file.
>>>
>>> HETATM    1  CAA DR0     1      83.043  46.127  36.820  1.00  0.00
>>> HETATM    2  CAB DR0     1      82.411  45.765  35.421  1.00  0.00
>>> HETATM    3  CAC DR0     1      81.495  46.822  34.598  1.00  0.00
>>> HETATM    4  CAD DR0     1      80.621  46.369  33.071  1.00  0.00
>>> HETATM    5  CAE DR0     1      79.305  47.302  32.172  1.00  0.00
>>> HETATM    6  CAF DR0     1      77.939  46.749  31.124  1.00  0.00
>>> HETATM    7  CAG DR0     1      76.264  47.439  30.612  1.00  0.00
>>> HETATM    8  CAH DR0     1      74.636  46.805  29.962  1.00  0.00
>>> HETATM    9  CAI DR0     1      72.805  47.674  30.179  1.00  0.00
>>> HETATM   10  CAJ DR0     1      73.794  48.838  31.123  1.00  0.00
>>> HETATM   11  OAK DR0     1      74.815  49.342  30.292  1.00  0.00
>>> HETATM   12  OAL DR0     1      74.592  48.143  32.194  1.00  0.00
>>> HETATM   13  CAM DR0     1      71.093  47.685  29.486  1.00  0.00
>>> HETATM   14  CAN DR0     1      71.598  47.212  28.208  1.00  0.00
>>> HETATM   15  OAO DR0     1      72.440  48.255  27.735  1.00  0.00
>>> HETATM   16  OAP DR0     1      72.374  46.050  28.399  1.00  0.00
>>> HETATM   17  CAA DRG     2      72.093  46.197  36.714  1.00  0.00
>>> HETATM   18  CAB DRG     2      71.418  45.759  35.400  1.00  0.00
>>> HETATM   19  CAC DRG     2      71.084  46.901  34.417  1.00  0.00
>>> HETATM   20  CAD DRG     2      70.620  46.251  33.139  1.00  0.00
>>> HETATM   21  CAE DRG     2      70.650  47.255  32.000  1.00  0.00
>>> HETATM   22  CAF DRG     2      69.655  46.512  30.955  1.00  0.00
>>> HETATM   23  CAG DRG     2      69.081  47.504  29.843  1.00  0.00
>>> HETATM   24  CAH DRG     2      67.208  47.518  29.256  1.00  0.00
>>> HETATM   25  CAI DRG     2      65.298  47.601  29.691  1.00  0.00
>>> HETATM   26  CAJ DRG     2      65.629  48.362  30.827  1.00  0.00
>>> HETATM   27  OAK DRG     2      65.140  49.590  30.429  1.00  0.00
>>> HETATM   28  OAL DRG     2      64.837  47.815  31.709  1.00  0.00
>>> HETATM   29  CAM DRG     2      63.041  47.557  29.333  1.00  0.00
>>> HETATM   30  CAN DRG     2      62.808  47.023  27.931  1.00  0.00
>>> HETATM   31  OAO DRG     2      63.130  48.142  27.185  1.00  0.00
>>> HETATM   32  OAP DRG     2      63.560  45.894  27.706  1.00  0.00
>>> HETATM   33  CAA DRG     3      61.174  46.188  36.668  1.00  0.00
>>> HETATM   34  CAB DRG     3      60.510  45.777  35.344  1.00  0.00
>>> HETATM   35  CAC DRG     3      60.221  46.928  34.352  1.00  0.00
>>> HETATM   36  CAD DRG     3      59.724  46.337  32.998  1.00  0.00
>>> HETATM   37  CAE DRG     3      60.252  47.307  31.985  1.00  0.00
>>> HETATM   38  CAF DRG     3      61.089  46.606  30.881  1.00  0.00
>>> HETATM   39  CAG DRG     3      60.868  47.564  29.740  1.00  0.00
>>> HETATM   40  CAH DRG     3      58.621  47.652  29.253  1.00  0.00
>>> HETATM   41  CAI DRG     3      56.328  47.703  29.755  1.00  0.00
>>> HETATM   42  CAJ DRG     3      55.914  48.516  30.963  1.00  0.00
>>> HETATM   43  OAK DRG     3      55.050  49.545  30.403  1.00  0.00
>>> HETATM   44  OAL DRG     3      54.945  47.724  31.565  1.00  0.00
>>> HETATM   45  CAM DRG     3      54.420  47.478  29.367  1.00  0.00
>>> HETATM   46  CAN DRG     3      53.587  47.142  27.983  1.00  0.00
>>> HETATM   47  OAO DRG     3      52.713  48.009  27.325  1.00  0.00
>>> HETATM   48  OAP DRG     3      53.396  45.805  27.517  1.00  0.00
>>> HETATM   49  CAA DR1     4      50.257  46.173  36.646  1.00  0.00
>>> HETATM   50  CAB DR1     4      49.673  45.778  35.270  1.00  0.00
>>> HETATM   51  CAC DR1     4      49.360  46.939  34.273  1.00  0.00
>>> HETATM   52  CAD DR1     4      49.270  46.480  32.735  1.00  0.00
>>> HETATM   53  CAE DR1     4      50.289  47.086  31.602  1.00  0.00
>>> HETATM   54  CAF DR1     4      51.813  46.713  31.234  1.00  0.00
>>> HETATM   55  CAG DR1     4      52.487  47.720  29.966  1.00  0.00
>>> HETATM   56  CAH DR1     4      50.870  47.989  29.178  1.00  0.00
>>> HETATM   57  CAI DR1     4      48.982  47.816  29.191  1.00  0.00
>>> HETATM   58  CAJ DR1     4      47.901  48.319  30.192  1.00  0.00
>>> HETATM   59  OAK DR1     4      47.004  49.132  29.503  1.00  0.00
>>> HETATM   60  OAL DR1     4      46.963  47.171  30.588  1.00  0.00
>>> HETATM   61  CAM DR1     4      47.752  46.922  28.157  1.00  0.00
>>> HETATM   62  CAN DR1     4      46.372  47.149  27.020  1.00  0.00
>>> HETATM   63  OAO DR1     4      45.018  47.950  26.877  1.00  0.00
>>> HETATM   64  OAP DR1     4      46.019  46.082  26.137  1.00  0.00
>>> TER
>>> ENDMDL
>>>
>>>
>>> --------------------------------------------------
>>> 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
>>>>>>
>>>>>> ========================================
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at http://www.gromacs.org/search before 
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>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>
>>>>>
>>>>
>>>> -- 
>>>> ========================================
>>>>
>>>> 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
>>>>
>>>> ========================================
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>> Please search the archive at http://www.gromacs.org/search before 
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>>>> Please don't post (un)subscribe requests to the list. Use the www 
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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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
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>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 

-- 
========================================

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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