[gmx-users] bad bond in polymer
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Aug 13 06:08:30 CEST 2009
nicegromacs wrote:
> Well, I tried to build a polymer with 3 monomers, DRG DR0 and DR1. In
> the pdb file They have the same order (DRG DR0 DR1). But when tried
> with pdb2gmx then I have the error:
> Fatal error:
> In the .rtp file in residue DR1 at line:
> CF1 CH3 0 1
There is no such line in the .rtp you provided. GROMACS would normally
provide more diagnostic information than this. Are you reading it all?
Are you using the right .rtp files?
> I changed the order of monomers to DR0 DRG DR1 with respect to the
> ''head'' monomer (DR0), Monomer of in the middle (DRG), and tail monomer
> (DR1), and the error no change. I have not changed the .hdb file.
>
> the estructure.ent
> HETATM 1 CAA DRG 1 58.110 44.852 36.809
This first residue listed is named as for your repeating unit. You need
to make sure the residue naming here matches your connectivity plan.
Mark
> HETATM 2 CAB DRG 1 56.934 44.517 35.875
> HETATM 3 CAC DRG 1 56.190 45.811 35.500
> HETATM 4 CAD DRG 1 55.051 45.476 34.520
> HETATM 5 CAE DRG 1 54.318 46.770 34.118
> HETATM 6 CAF DRG 1 53.310 46.438 33.003
> HETATM 7 CAG DRG 1 52.657 47.686 32.473
> HETATM 8 CAH DRG 1 53.521 48.753 31.851
> HETATM 9 CAI DRG 1 54.199 48.265 30.599
> HETATM 10 CAJ DRG 1 55.615 47.887 30.630
> HETATM 11 OAK DRG 1 56.231 47.370 29.495
> HETATM 12 OAL DRG 1 56.359 48.028 31.798
> HETATM 13 CAM DRG 1 53.423 48.169 29.314
> HETATM 14 CAN DRG 1 52.529 46.963 29.306
> HETATM 15 OAO DRG 1 53.058 45.698 29.542
> HETATM 16 OAP DRG 1 51.206 47.090 28.902
> HETATM 17 CA1 DR0 1 43.743 50.975 25.947
> HETATM 18 CA2 DR0 1 44.674 51.739 26.906
> HETATM 19 CA3 DR0 1 45.313 50.749 27.897
> HETATM 20 CA4 DR0 1 46.248 51.508 28.856
> HETATM 21 CA5 DR0 1 46.862 50.512 29.856
> HETATM 22 CA6 DR0 1 47.789 51.264 30.830
> HETATM 23 CA7 DR0 1 48.356 50.315 31.851
> HETATM 24 CA8 DR0 1 49.361 49.293 31.385
> HETATM 25 CA9 DR0 1 50.545 49.110 32.302
> HETATM 26 C10 DR0 1 51.122 50.259 33.020
> HETATM 27 O12 DR0 1 50.919 51.560 32.571
> HETATM 28 O11 DR0 1 51.877 50.069 34.174
> HETATM 29 C13 DR0 1 51.189 47.782 32.378
> HETATM 30 C14 DR0 1 50.382 46.559 32.210
> HETATM 31 O16 DR0 1 50.972 45.336 31.910
> HETATM 32 O15 DR0 1 48.997 46.595 32.315
> HETATM 33 CF1 DR1 1 55.642 46.172 39.128
> HETATM 34 CF2 DR1 1 54.229 46.780 39.194
> HETATM 35 CF3 DR1 1 53.591 46.765 37.791
> HETATM 36 CF4 DR1 1 52.185 47.384 37.876
> HETATM 37 CF5 DR1 1 51.526 47.395 36.484
> HETATM 38 CF6 DR1 1 50.134 48.044 36.601
> HETATM 39 CF7 DR1 1 49.475 48.098 35.212
> HETATM 40 CF8 DR1 1 48.132 48.846 35.298
> HETATM 41 CF9 DR1 1 47.562 49.035 33.918
> HETATM 42 C1F DR1 1 46.647 48.028 33.366
> HETATM 43 O3F DR1 1 46.397 46.849 34.062
> HETATM 44 O2F DR1 1 45.998 48.241 32.154
> HETATM 45 C4F DR1 1 47.798 50.304 33.215
> HETATM 46 C5F DR1 1 47.426 51.565 33.874
> HETATM 47 O7F DR1 1 47.843 52.791 33.365
> HETATM 48 O6F DR1 1 46.661 51.551 35.036
> CONECT 1 2
> CONECT 2 1 3
> CONECT 3 2 4
> CONECT 4 3 5
> CONECT 5 4 6
> CONECT 6 5 7
> CONECT 7 6 8 29
> CONECT 8 7 9
> CONECT 9 8 10 13
> CONECT 10 9 11 12
> CONECT 11 10
> CONECT 12 10
> CONECT 13 9 14
> CONECT 14 13 15 16
> CONECT 15 14
> CONECT 16 14
> CONECT 17 18
> CONECT 18 17 19
> CONECT 19 18 20
> CONECT 20 19 21
> CONECT 21 20 22
> CONECT 22 21 23
> CONECT 23 22 24 45
> CONECT 24 23 25
> CONECT 25 24 26 29
> CONECT 26 25 27 28
> CONECT 27 26
> CONECT 28 26
> CONECT 29 25 30 7
> CONECT 30 29 31 32
> CONECT 31 30
> CONECT 32 30
> CONECT 33 34
> CONECT 34 33 35
> CONECT 35 34 36
> CONECT 36 35 37
> CONECT 37 36 38
> CONECT 38 37 39
> CONECT 39 38 40
> CONECT 40 39 41
> CONECT 41 40 42 45
> CONECT 42 41 43 44
> CONECT 43 42
> CONECT 44 42
> CONECT 45 41 46 23
> CONECT 46 45 47 48
> CONECT 47 46
> CONECT 48 46
> END
> and the .rtp
>
> [ DRG ] ; unidad
> [ atoms ]
> CAA CH3 0.00
> CAB CH2 0.00
> CAC CH2 0.00
> CAD CH2 0.00
> CAE CH2 0.00
> CAF CH2 0.00
> CAG CH1 0.00
> CAH CH2 0.04
> CAI CH1 0.10
> CAJ C 0.35
> OAK OM -0.75
> OAL OM -0.75
> CAM CH2 0.04
> CAN C 0.37
> OAO OM -0.70
> OAP OM -0.70
> [ 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 C
> -CAM -CAN -CAI C
> CAJ CAI OAL O
> CAN CAM OAP O
> CAI CAH CAJ C
>
> [ DR0 ] ;head of
> [ atoms ]
> CA1 CH3 0.00
> CA2 CH2 0.00
> CA3 CH2 0.00
> CA4 CH2 0.00
> CA5 CH2 0.00
> CA6 CH2 0.00
> CA7 CH2 0.00
> CA8 CH2 0.04
> CA9 CH1 0.10
> C10 C 0.35
> O12 OM -0.75
> O11 OM -0.75
> C13 CH2 0.04
> C14 C 0.37
> O16 OM -0.70
> O15 OM -0.70
> [ bonds ]
> CA1 CA2
> CA2 CA3
> CA3 CA4
> CA4 CA5
> CA5 CA6
> CA6 CA7
> CA7 CA8
> CA8 CA9
> CA9 C10
> CA9 C13
> C10 O12
> C10 O11
> C13 C14
> C14 O16
> C14 O15
> CA7 +CAM
> [ impropers ]
> CA7 CA6 +CAM CA8
> +CAM +CAI +CAN CA7
> C10 CA9 O11 O12
> C14 C13 O15 O16
> CA9 CA8 C10 C13
>
> [ DR1 ] ; tail of t
> CF1 CH3 0.00
> CF2 CH2 0.00
> CF3 CH2 0.00
> CF4 CH2 0.00
> CF5 CH2 0.00
> CF6 CH2 0.00
> CF7 CH2 0.00
> CF8 CH2 0.04
> CF9 CH1 0.10
> C1F C 0.35
> O3F OM -0.75
> O2F OM -0.75
> C4F CH2 0.04
> C5F C 0.37
> O7F OM -0.70
> O6F OM -0.70
> [ bonds ]
> C4F -CAG
> CF1 CF2
> CF2 CF3
> CF3 CF4
> CF4 CF5
> CF5 CF6
> CF6 CF7
> CF7 CF8
> CF8 CF9
> CF9 C1F
> CF9 C4F
> C1F O3F
> C1F O2F
> C4F C5F
> C5F O7F
> C5F O6F
> [ impropers ]
> C4F C5F CF9 -CAG
> -CAG -CAF -CAH C4F
> C1F CF9 O2F O3F
> C5F C4F O6F O7F
> CF9 CF8 C1F C4F
>
>
> --------------------------------------------------
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Sent: Wednesday, August 12, 2009 9:50 PM
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] bad bond in polymer
>
>>
>>
>> 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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