[gmx-users] bad bond in polymer
nicegromacs
nicegromacs at live.cl
Thu Aug 13 05:57:13 CEST 2009
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
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
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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