[gmx-users] Problem building a new polymer using pdb2gmx ....
David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 17 21:09:49 CEST 2008
Alberto Sergio Garay wrote:
> Dear David (van der Spoel)
>
> Thank you for help again!
>
> I'm sending a part of my gro input file, which includes the first 2
> residues. The VBT 2 is the one which pdb2gmx complains about:
try renaming your OT1 to OX1 or something like this. pdb2gmx might think
it is an O-terminal (as you have in proteins)
>
> pdb2gmx -f polymer.gro -ter -ignh -p top
>
> Processing chain 1 (239 atoms, 14 residues)
> Fatal error:
> Atom O in residue VBT 2 not found in rtp entry with 24 atoms
> while sorting atoms
>
> Generated by trjconv : 14 TEQ-VBT 1:1 t= 0000.00000
> 309
> 1TQL CTL 1 3.058 5.402 1.733
> 1TQL CC2 2 3.144 5.276 1.717
> 1TQL CR1 3 3.225 5.235 1.822
> 1TQL CR2 4 3.184 5.124 1.894
> 1TQL HR2 5 3.092 5.069 1.874
> 1TQL CR3 6 3.257 5.086 2.006
> 1TQL HR3 7 3.237 4.993 2.060
> 1TQL CR4 8 3.373 5.150 2.048
> 1TQL CR5 9 3.414 5.263 1.977
> 1TQL HR5 10 3.510 5.311 1.994
> 1TQL CR6 11 3.337 5.303 1.869
> 1TQL HR6 12 3.370 5.401 1.832
> 1TQL CN4 13 3.439 5.090 2.154
> 1TQL N 14 3.558 5.089 2.242
> 1TQL CN1 15 3.575 5.230 2.281
> 1TQL CN2 16 3.664 5.062 2.144
> 1TQL CN3 17 3.522 4.977 2.330
> 1TQL CE1 18 3.523 5.373 2.263
> 1TQL CE2 19 3.817 5.054 2.153
> 1TQL CE3 20 3.588 4.905 2.448
> 2VBT CC1 21 3.221 5.305 1.589
> 2VBT CC2 22 3.143 5.334 1.460
> 2VBT CR1 23 3.115 5.221 1.384
> 2VBT CR2 24 3.196 5.155 1.293
> 2VBT HR2 25 3.305 5.159 1.298
> 2VBT CR3 26 3.132 5.074 1.200
> 2VBT HR3 27 3.198 5.003 1.151
> 2VBT CR4 28 2.995 5.068 1.175
> 2VBT CT1 29 2.948 5.023 1.052
> 2VBT NT1 30 3.028 5.038 0.928
> 2VBT CR5 31 2.919 5.144 1.263
> 2VBT HR5 32 2.810 5.142 1.268
> 2VBT CR6 33 2.977 5.208 1.372
> 2VBT HR6 34 2.916 5.232 1.459
> 2VBT CT2 35 3.070 4.916 0.874
> 2VBT HT1 36 3.009 4.827 0.860
> 2VBT CT3 37 3.190 4.911 0.804
> 2VBT CT4 38 3.245 4.779 0.750
> 2VBT CT5 39 3.264 5.027 0.784
> 2VBT OT1 40 3.364 5.030 0.712
> ........................................
>
> Below it is a part of the rtp file which includes the VBT building block:
>
> [ VBT ]
> [ atoms ]
> ; name type charge chargegroup
> CC1 CH2 0.00000 1
> CC2 CH1 0.12000 2
> CR1 C -0.12000 3
> CR2 C -0.14000 4
> HR2 HC 0.14000 4
> CR3 C -0.08000 5
> HR3 HC 0.08000 5
> CR4 C -0.05000 6
> CT1 CH2 0.37000 6
> NT1 NR -0.32000 6
> CR5 C -0.13000 7
> HR5 HC 0.13000 7
> CR6 C -0.17000 8
> HR6 HC 0.17000 8
> CT2 C -0.21000 9
> HT1 HC 0.21000 9
> CT3 C -0.09000 10
> CT4 CH3 0.09000 10
> CT5 C 0.58000 11
> OT1 O -0.58000 11
> NT2 NR -0.22000 12
> HT2 H 0.22000 12
> CT6 C 0.54000 13
> OT2 O -0.54000 13
> ;
> [ bonds ]
> ; atom1 atom2 b0 kb
> CC2 +CC1 gb_27
> CC1 CC2 gb_27
> CC2 CR1 gb_15
> CR1 CR2 gb_16
> CR2 CR3 gb_16
> CR3 CR4 gb_16
> CR4 CR5 gb_16
> CR5 CR6 gb_16
> CR6 CR1 gb_16
> CR2 HR2 gb_3
> CR3 HR3 gb_3
> CR5 HR5 gb_3
> CR6 HR6 gb_3
> CR4 CT1 gb_15
> CT1 NT1 gb_23
> NT1 CT2 gb_17
> CT2 HT1 gb_3
> CT2 CT3 gb_16
> CT3 CT4 gb_27
> CT3 CT5 gb_16
> CT5 OT1 gb_5
> CT5 NT2 gb_17
> NT2 HT2 gb_2
> NT2 CT6 gb_17
> CT6 OT2 gb_5
> CT6 NT1 gb_17
>
> [ angles ]
> ; ai aj ak gromos type
> -CC2 CC1 CC2 ga_15
> CC1 CC2 +CC1 ga_15
> CR1 CC2 +CC1 ga_15
> CC1 CC2 CR1 ga_15
> CC2 CR1 CR2 ga_25
> CC2 CR1 CR6 ga_25
> CR1 CR2 CR3 ga_27
> CR2 CR3 CR4 ga_27
> CR3 CR4 CR5 ga_27
> CR4 CR5 CR6 ga_27
> CR5 CR6 CR1 ga_27
> CR6 CR1 CR2 ga_27
> CR1 CR2 HR2 ga_25
> HR2 CR2 CR3 ga_25
> CR2 CR3 HR3 ga_25
> HR3 CR3 CR4 ga_25
> CR4 CR5 HR5 ga_25
> HR5 CR5 CR6 ga_25
> CR5 CR6 HR6 ga_25
> HR6 CR6 CR1 ga_25
> CR3 CR4 CT1 ga_25
> CR5 CR4 CT1 ga_25
> CR4 CT1 NT1 ga_8
> CT1 NT1 CT2 ga_27
> CT1 NT1 CT6 ga_27
> NT1 CT2 HT1 ga_25
> NT1 CT2 CT3 ga_27
> NT1 CT6 OT2 ga_27
> NT1 CT6 NT2 ga_27
> HT1 CT2 CT3 ga_25
> CT2 CT3 CT4 ga_27
> CT2 CT3 CT5 ga_27
> CT4 CT3 CT5 ga_27
> CT3 CT5 OT1 ga_27
> CT3 CT5 NT2 ga_27
> OT1 CT5 NT2 ga_27
> CT5 NT2 HT2 ga_25
> CT6 NT2 HT2 ga_25
> CT5 NT2 CT6 ga_27
> NT2 CT6 OT2 ga_27
> CT6 NT1 CT2 ga_27
> -CCE CC2 +CC1 ga_15
> -CCE CC2 CR1 ga_15
> ;
> [ impropers ]
> ; ai aj ak al gromos type
> CC2 CC1 CR1 +CC1 gi_2
> ; tymine ring:
> ; sustituyents
> NT1 CT6 CT2 CT1 gi_1
> CT6 NT1 NT2 OT2 gi_1
> CT2 NT1 CT3 HT1 gi_1
> CT3 CT2 CT5 CT4 gi_1
> CT5 CT3 NT2 OT1 gi_1
> NT2 CT5 CT6 HT2 gi_1
> ; ring
> NT1 CT2 CT3 CT5 gi_1
> CT2 CT3 CT5 NT2 gi_1
> CT3 CT5 NT2 CT6 gi_1
> CT5 NT2 CT6 NT1 gi_1
> NT2 CT6 NT1 CT2 gi_1
> CT6 NT1 CT2 CT3 gi_1
> ;
> ; bencene ring:
> ; sustituyents
> CR1 CR6 CR3 CC2 gi_1
> CR4 CR3 CR5 CT1 gi_1
> CR2 CR1 CR3 HR2 gi_1
> CR3 CR2 CR4 HR3 gi_1
> CR5 CR4 CR6 HR5 gi_1
> CR6 CR5 CR1 HR6 gi_1
> ; ring
> CR1 CR2 CR3 CR4 gi_1
> CR2 CR3 CR4 CR5 gi_1
> CR3 CR4 CR5 CR6 gi_1
> CR4 CR5 CR6 CR1 gi_1
> CR5 CR6 CR1 CR2 gi_1
> CR6 CR1 CR2 CR3 gi_1
> ;
> ;
> [ dihedrals ]
> ; ai aj ak al gromos type
> -CC1 -CC2 CC1 CC2 gd_34
> -CC2 CC1 CC2 +CC1 gd_34
> -CC2 CC1 CC2 CR1 gd_34
> CR3 CR4 CT1 NT1 gd_10
> CR4 CT1 NT1 CT2 gd_40
> CC1 CC2 CR1 CR2 gd_40
>
> [ exclusions ]
> ; ai aj
> CC2 HR2
> CC2 CR3
> CC2 HR6
> CC2 CR5
> CR1 HR3
> CR1 HR5
> CR1 CR4
> CR2 HR6
> CR2 CT1
> HR2 HR3
> HR2 CR4
> HR2 CR6
> CR6 CT1
> CR6 CR3
> CR3 HR5
> CR3 NT1 ; CHECK
> HR3 CR5
> HR3 CT1
> CR4 CT2
> CR4 CT6
> CT1 HT1
> CT1 CT3
> CT1 NT2
> CT1 OT2
> NT1 CT4
> NT1 CT5
> NT1 HT2
> CT2 OT1
> CT2 NT2
> CT2 OT2
> HT1 CT4
> HT1 CT6
> HT1 CT5
> CT6 CT3
> CT6 OT1
> CT4 OT1
> CT4 NT2
>
> I tested the integrity of the rtp file using the pdb2gmx in a pdb protein
> file, and it did it right.
>
> Below it is a part of the aminoacid.dat file where I include the names
> of the residues
> building block.
>
> 60
> ABU
> ACE
> AIB
> ALA
> ARG
> ARGN
> ...
> ...
> VBT
> VBL
> VBR
> TEQ
> TQL
> TQR
>
> Finally a replace the original rtp and aminoacid files for the ones that
> I've posted.
>
> Thank you and I'll be waiting anxiously for any clue for my problem.
>
>
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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