[gmx-users] pdb file from prodrg2 cannot be recognized by gromacs?
Yafei Dai
ydai at gmu.edu
Wed Sep 5 04:51:31 CEST 2007
I got a pdb file from prodrg2 and I did pdb2gmx:
pdb2gmx -f test.pdb -p test.top -o test.gro
I was told "DRG" not found in residue topology. What can I do for this error information? My pdb file is as below:
REMARK
REMARK
REMARK This file was generated by PRODRG version 061128.0522
REMARK PRODRG written/copyrighted by Daan van Aalten
REMARK and Alexander Schuettelkopf
REMARK
REMARK Questions/comments to dava at davapc1.bioch.dundee.ac.uk
REMARK
REMARK When using this software in a publication, cite:
REMARK A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK PRODRG - a tool for high-throughput crystallography
REMARK of protein-ligand complexes.
REMARK Acta Crystallogr. D60, 1355--1363.
REMARK
REMARK
HETATM 1 NAK DRG 1 15.040 1.790 -0.060 1.00 20.00 N
HETATM 2 HAA DRG 1 15.040 0.790 -0.070 1.00 20.00 H
HETATM 3 CAC DRG 1 16.110 2.570 -0.040 1.00 20.00 C
HETATM 4 1HAC DRG 1 17.061 2.262 -0.040 1.00 20.00 H
HETATM 5 CAA DRG 1 15.700 3.830 -0.020 1.00 20.00 C
HETATM 6 1HAA DRG 1 16.288 4.639 -0.001 1.00 20.00 H
HETATM 7 CAE DRG 1 14.370 3.830 -0.030 1.00 20.00 C
HETATM 8 1HAE DRG 1 13.784 4.641 -0.024 1.00 20.00 H
HETATM 9 CAO DRG 1 13.950 2.560 -0.050 1.00 20.00 C
HETATM 10 CAQ DRG 1 12.620 2.120 -0.050 1.00 20.00 C
HETATM 11 NAM DRG 1 11.530 2.890 -0.040 1.00 20.00 N
HETATM 12 HAC DRG 1 11.530 3.890 -0.020 1.00 20.00 H
HETATM 13 CAG DRG 1 12.210 0.850 -0.080 1.00 20.00 C
HETATM 14 1HAG DRG 1 12.798 0.042 -0.105 1.00 20.00 H
HETATM 15 CAI DRG 1 10.880 0.850 -0.070 1.00 20.00 C
HETATM 16 1HAI DRG 1 10.298 0.037 -0.076 1.00 20.00 H
HETATM 17 CAS DRG 1 10.450 2.110 -0.050 1.00 20.00 C
HETATM 18 CAT DRG 1 9.120 2.530 -0.040 1.00 20.00 C
HETATM 19 NAN DRG 1 8.040 1.740 -0.050 1.00 20.00 N
HETATM 20 HAD DRG 1 8.060 0.740 -0.070 1.00 20.00 H
HETATM 21 CAJ DRG 1 8.680 3.780 -0.010 1.00 20.00 C
HETATM 22 1HAJ DRG 1 9.252 4.600 0.003 1.00 20.00 H
HETATM 23 CAH DRG 1 7.350 3.760 0.000 1.00 20.00 C
HETATM 24 1HAH DRG 1 6.753 4.562 0.026 1.00 20.00 H
HETATM 25 CAR DRG 1 6.950 2.490 -0.030 1.00 20.00 C
HETATM 26 CAP DRG 1 5.620 2.030 -0.030 1.00 20.00 C
HETATM 27 CAF DRG 1 5.220 0.760 -0.040 1.00 20.00 C
HETATM 28 1HAF DRG 1 5.820 -0.040 -0.046 1.00 20.00 H
HETATM 29 CAB DRG 1 3.890 0.730 -0.040 1.00 20.00 C
HETATM 30 1HAB DRG 1 3.317 -0.090 -0.059 1.00 20.00 H
HETATM 31 CAD DRG 1 3.460 1.990 -0.010 1.00 20.00 C
HETATM 32 1HAD DRG 1 2.504 2.283 0.009 1.00 20.00 H
HETATM 33 NAL DRG 1 4.520 2.790 -0.010 1.00 20.00 N
HETATM 34 HAB DRG 1 4.500 3.790 0.010 1.00 20.00 H
CONECT 1 2 3 9
CONECT 2 1
CONECT 3 1 4 5
CONECT 4 3
CONECT 5 3 6 7
CONECT 6 5
CONECT 7 5 8 9
CONECT 8 7
CONECT 9 1 7 10
CONECT 10 9 11 13
CONECT 11 10 12 17
CONECT 12 11
CONECT 13 10 14 15
CONECT 14 13
CONECT 15 13 16 17
CONECT 16 15
CONECT 17 11 15 18
CONECT 18 17 19 21
CONECT 19 18 20 25
CONECT 20 19
CONECT 21 18 22 23
CONECT 22 21
CONECT 23 21 24 25
CONECT 24 23
CONECT 25 19 23 26
CONECT 26 25 27 33
CONECT 27 26 28 29
CONECT 28 27
CONECT 29 27 30 31
CONECT 30 29
CONECT 31 29 32 33
CONECT 32 31
CONECT 33 26 31 34
CONECT 34 33
END
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