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:
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.
--
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221
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