Again thank you so much sir for your valuable advice.
Sir, I have overcome the above problem by remodeling the protein and
topol.top (2.5 MB)
unk1(itp).dat (10.7 KB)
unk1(prm).dat (889 Bytes)
successfully created protein topology file. But I have another error during creating ions.tpr file.
Here is the error.
ruhul@ruhul:~/MD/ACE_YY$ gmx grompp -f ions.mdp -c complex_solv.gro -p topol.top -o ions.tpr
:-) GROMACS - gmx grompp, 2021.4-Ubuntu-2021.4-2 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
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Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
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GROMACS: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/ruhul/MD/ACE_YY
Command line:
gmx grompp -f ions.mdp -c complex_solv.gro -p topol.top -o ions.tpr
Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’
NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to -973478741
ERROR 1 [file unk1.prm, line 4]:
Unknown bond_atomtype OGTIP3
There was 1 note
Program: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 763)
Fatal error:
There was 1 error in input file(s)
Here, I have attached toplogy file, ligand itp and prm file.
Sir, please suggest me what should I do.
Presumably OGTIP3 is some generic form of the atom type for TIP3P oxygen. I don’t understand what is in your ligand topology because it appears to be some mix of organic compound, dummy atoms, and water. I would revisit what it is that you’re doing and trying to parametrize, because it looks very strange and scrambled.
Hello,
I have the similar problem I want to pass a closed circular dna to pdb2gmx. I put TER at the end of each chain and change the name of the first and last residue according to the rtp. I got this error. Could you please help me?
it is the pdb file:
ATOM 1 P DG 1 -0.061 9.257 -1.748 1.00 0.00 P
ATOM 2 O5’ DG 1 -0.729 8.303 -0.917 1.00 0.00 O
ATOM 3 C5’ DG 1 -1.729 7.939 -1.894 1.00 0.00 C
ATOM 4 H5’ DG 1 -1.338 7.283 -2.668 1.00 0.00 H
ATOM 5 H5’2 DG 1 -2.049 8.849 -2.388 1.00 0.00 H
ATOM 6 C4’ DG 1 -2.966 7.227 -1.357 1.00 0.00 C
ATOM 7 H4’ DG 1 -3.826 7.504 -1.965 1.00 0.00 H
ATOM 8 O4’ DG 1 -2.743 5.835 -1.463 1.00 0.00 O
ATOM 9 C1’ DG 1 -2.477 5.348 -0.170 1.00 0.00 C
ATOM 10 H1’ DG 1 -3.323 4.747 0.169 1.00 0.00 H
ATOM 11 N9 DG 1 -1.301 4.509 -0.108 1.00 0.00 N
ATOM 12 C8 DG 1 0.018 4.869 -0.039 1.00 0.00 C
ATOM 13 H8 DG 1 0.337 5.899 -0.005 1.00 0.00 H
ATOM 14 N7 DG 1 0.832 3.863 -0.035 1.00 0.00 N
ATOM 15 C5 DG 1 -0.038 2.760 -0.021 1.00 0.00 C
ATOM 16 C6 DG 1 0.213 1.362 0.005 1.00 0.00 C
ATOM 17 O6 DG 1 1.301 0.807 0.006 1.00 0.00 O
ATOM 18 N1 DG 1 -0.930 0.584 0.009 1.00 0.00 N
ATOM 19 H1 DG 1 -0.809 -0.415 0.011 1.00 0.00 H
ATOM 20 C2 DG 1 -2.189 1.075 0.008 1.00 0.00 C
ATOM 21 N2 DG 1 -3.186 0.235 -0.008 1.00 0.00 N
ATOM 22 H21 DG 1 -3.018 -0.772 -0.009 1.00 0.00 H
ATOM 23 H22 DG 1 -4.112 0.613 0.037 1.00 0.00 H
ATOM 24 N3 DG 1 -2.475 2.372 0.016 1.00 0.00 N
ATOM 25 C4 DG 1 -1.349 3.154 -0.020 1.00 0.00 C
ATOM 26 C3’ DG 1 -3.147 7.601 0.111 1.00 0.00 C
ATOM 27 H3’ DG 1 -2.743 8.599 0.312 1.00 0.00 H
ATOM 28 C2’ DG 1 -2.353 6.499 0.782 1.00 0.00 C
ATOM 29 H2’ DG 1 -1.366 6.878 1.023 1.00 0.00 H
ATOM 30 H2’2 DG 1 -2.791 6.091 1.677 1.00 0.00 H
ATOM 31 O3’ DG 1 -4.434 7.553 0.610 1.00 0.00 O
ATOM 32 OP2 DG 1 -0.966 10.438 -1.514 1.00 0.00 O
ATOM 33 OP1 DG 1 1.207 9.574 -1.267 1.00 0.00 O
…
ATOM 2798 P DT 89 5.168 7.728 -4.683 1.00 0.00 P
ATOM 2799 OP1 DT 89 5.523 9.146 -4.724 1.00 0.00 O
ATOM 2800 OP2 DT 89 5.826 6.792 -3.726 1.00 0.00 O1-
ATOM 2801 O5’ DT 89 3.590 7.436 -4.607 1.00 0.00 O
ATOM 2802 C5’ DT 89 2.675 7.686 -5.682 1.00 0.00 C
ATOM 2803 H5’ DT 89 2.709 6.901 -6.440 1.00 0.00 H
ATOM 2804 H5’2 DT 89 2.939 8.621 -6.168 1.00 0.00 H
ATOM 2805 C4’ DT 89 1.245 7.758 -5.150 1.00 0.00 C
ATOM 2806 H4’ DT 89 0.673 8.427 -5.793 1.00 0.00 H
ATOM 2807 O4’ DT 89 0.642 6.472 -5.187 1.00 0.00 O
ATOM 2808 C1’ DT 89 0.600 5.926 -3.884 1.00 0.00 C
ATOM 2809 H1’ DT 89 -0.453 5.851 -3.612 1.00 0.00 H
ATOM 2810 N1 DT 89 1.129 4.548 -3.799 1.00 0.00 N
ATOM 2811 C6 DT 89 2.477 4.293 -3.660 1.00 0.00 C
ATOM 2812 H6 DT 89 3.162 5.123 -3.622 1.00 0.00 H
ATOM 2813 C5 DT 89 2.936 3.016 -3.576 1.00 0.00 C
ATOM 2814 C7 DT 89 4.411 2.708 -3.447 1.00 0.00 C
ATOM 2815 H71 DT 89 4.869 3.249 -2.627 1.00 0.00 H
ATOM 2816 H72 DT 89 4.587 1.635 -3.372 1.00 0.00 H
ATOM 2817 H73 DT 89 4.895 2.949 -4.358 1.00 0.00 H
ATOM 2818 C4 DT 89 2.017 1.904 -3.607 1.00 0.00 C
ATOM 2819 O4 DT 89 2.344 0.732 -3.559 1.00 0.00 O
ATOM 2820 N3 DT 89 0.691 2.240 -3.685 1.00 0.00 N
ATOM 2821 H3 DT 89 0.017 1.495 -3.674 1.00 0.00 H
ATOM 2822 C2 DT 89 0.192 3.510 -3.766 1.00 0.00 C
ATOM 2823 O2 DT 89 -1.026 3.680 -3.786 1.00 0.00 O
ATOM 2824 C3’ DT 89 1.241 8.272 -3.700 1.00 0.00 C
ATOM 2825 H3’ DT 89 2.159 8.825 -3.488 1.00 0.00 H
ATOM 2826 C2’ DT 89 1.231 6.935 -2.926 1.00 0.00 C
ATOM 2827 H2’ DT 89 2.237 6.683 -2.592 1.00 0.00 H
ATOM 2828 H2’2 DT 89 0.642 6.884 -2.040 1.00 0.00 H
ATOM 2829 O3’ DT 89 0.160 9.167 -3.501 1.00 0.00 O
TER 2830 DT 89
ATOM 2831 P DA 90 -5.287 -7.085 -1.012 1.00 0.00 P
ATOM 2832 O5’ DA 90 -5.115 -6.424 -2.658 1.00 0.00 O
ATOM 2833 C5’ DA 90 -5.883 -5.639 -1.744 1.00 0.00 C
ATOM 2834 H5’ DA 90 -5.241 -5.272 -0.934 1.00 0.00 H
ATOM 2835 H5’2 DA 90 -6.628 -6.284 -1.284 1.00 0.00 H
ATOM 2836 C4’ DA 90 -6.563 -4.438 -2.445 1.00 0.00 C
ATOM 2837 H4’ DA 90 -7.494 -4.208 -1.921 1.00 0.00 H
ATOM 2838 O4’ DA 90 -5.650 -3.371 -2.246 1.00 0.00 O
ATOM 2839 C1’ DA 90 -5.005 -3.129 -3.472 1.00 0.00 C
ATOM 2840 H1’ DA 90 -5.375 -2.174 -3.850 1.00 0.00 H
ATOM 2841 N9 DA 90 -3.556 -3.038 -3.425 1.00 0.00 N
ATOM 2842 C8 DA 90 -2.617 -4.040 -3.461 1.00 0.00 C
ATOM 2843 H8 DA 90 -2.894 -5.080 -3.487 1.00 0.00 H
ATOM 2844 N7 DA 90 -1.386 -3.626 -3.449 1.00 0.00 N
ATOM 2845 C5 DA 90 -1.560 -2.231 -3.494 1.00 0.00 C
ATOM 2846 C6 DA 90 -0.693 -1.132 -3.533 1.00 0.00 C
ATOM 2847 N6 DA 90 0.606 -1.289 -3.495 1.00 0.00 N
ATOM 2848 H61 DA 90 1.202 -0.475 -3.553 1.00 0.00 H
ATOM 2849 H62 DA 90 0.987 -2.209 -3.448 1.00 0.00 H
ATOM 2850 N1 DA 90 -1.146 0.116 -3.610 1.00 0.00 N
ATOM 2851 C2 DA 90 -2.460 0.311 -3.665 1.00 0.00 C
ATOM 2852 H2 DA 90 -2.802 1.337 -3.734 1.00 0.00 H
ATOM 2853 N3 DA 90 -3.401 -0.616 -3.641 1.00 0.00 N
ATOM 2854 C4 DA 90 -2.869 -1.868 -3.535 1.00 0.00 C
ATOM 2855 C3’ DA 90 -6.730 -4.744 -3.975 1.00 0.00 C
ATOM 2856 H3’ DA 90 -6.837 -5.827 -4.088 1.00 0.00 H
ATOM 2857 C2’ DA 90 -5.405 -4.171 -4.473 1.00 0.00 C
ATOM 2858 H2’ DA 90 -4.717 -4.977 -4.712 1.00 0.00 H
ATOM 2859 H2’2 DA 90 -5.467 -3.552 -5.352 1.00 0.00 H
ATOM 2860 O3’ DA 90 -7.677 -4.225 -4.879 1.00 0.00 O
ATOM 2861 OP1 DA 90 -5.707 -6.411 0.194 1.00 0.00 O
ATOM 2862 OP2 DA 90 -6.292 -8.222 -1.187 1.00 0.00 O
…
ATOM 5620 O3’ DA 177 0.590 -8.874 2.929 1.00 0.00 O
ATOM 5621 P DC 178 0.681 -9.097 1.319 1.00 0.00 P
ATOM 5622 OP1 DC 178 0.480 -10.468 1.012 1.00 0.00 O
ATOM 5623 OP2 DC 178 1.876 -8.344 0.715 1.00 0.00 O1-
ATOM 5624 O5’ DC 178 -0.586 -8.172 0.931 1.00 0.00 O
ATOM 5625 C5’ DC 178 -1.571 -7.830 1.915 1.00 0.00 C
ATOM 5626 H5’ DC 178 -1.170 -7.142 2.652 1.00 0.00 H
ATOM 5627 H5’2 DC 178 -1.857 -8.736 2.438 1.00 0.00 H
ATOM 5628 C4’ DC 178 -2.813 -7.167 1.348 1.00 0.00 C
ATOM 5629 H4’ DC 178 -3.649 -7.435 1.992 1.00 0.00 H
ATOM 5630 O4’ DC 178 -2.677 -5.758 1.348 1.00 0.00 O
ATOM 5631 C1’ DC 178 -2.432 -5.303 0.035 1.00 0.00 C
ATOM 5632 H1’ DC 178 -3.294 -4.699 -0.259 1.00 0.00 H
ATOM 5633 N1 DC 178 -1.240 -4.421 0.008 1.00 0.00 N
ATOM 5634 C6 DC 178 0.042 -4.917 0.007 1.00 0.00 C
ATOM 5635 H6 DC 178 0.211 -5.987 0.020 1.00 0.00 H
ATOM 5636 C5 DC 178 1.095 -4.065 0.008 1.00 0.00 C
ATOM 5637 H5 DC 178 2.102 -4.445 0.012 1.00 0.00 H
ATOM 5638 C4 DC 178 0.811 -2.682 0.006 1.00 0.00 C
ATOM 5639 N4 DC 178 1.787 -1.837 -0.023 1.00 0.00 N
ATOM 5640 H41 DC 178 1.553 -0.849 -0.005 1.00 0.00 H
ATOM 5641 H42 DC 178 2.731 -2.147 0.021 1.00 0.00 H
ATOM 5642 N3 DC 178 -0.404 -2.187 -0.004 1.00 0.00 N
ATOM 5643 C2 DC 178 -1.450 -3.038 0.001 1.00 0.00 C
ATOM 5644 O2 DC 178 -2.580 -2.547 -0.014 1.00 0.00 O
ATOM 5645 C3’ DC 178 -3.048 -7.638 -0.085 1.00 0.00 C
ATOM 5646 H3’ DC 178 -2.550 -8.595 -0.261 1.00 0.00 H
ATOM 5647 C2’ DC 178 -2.398 -6.516 -0.897 1.00 0.00 C
ATOM 5648 H2’ DC 178 -1.397 -6.801 -1.223 1.00 0.00 H
ATOM 5649 H2’2 DC 178 -2.958 -6.257 -1.772 1.00 0.00 H
ATOM 5650 O3’ DC 178 -4.429 -7.771 -0.343 1.00 0.00 O
TER 5651 DC 178
CONECT 1 2 2829 32 33
CONECT 2 1 3
CONECT 3 2 4 5 6
CONECT 4 3
CONECT 5 3
CONECT 6 3 8 7 26
CONECT 7 6
CONECT 8 6 9
CONECT 9 8 11 28 10
CONECT 10 9
CONECT 11 9 12 25
CONECT 12 11 14 13
CONECT 13 12
CONECT 14 12 15
CONECT 15 14 25 16
CONECT 16 15 17 18
CONECT 17 16
CONECT 18 16 20 19
CONECT 19 18
CONECT 20 18 24 21
CONECT 21 20 22 23
CONECT 22 21
CONECT 23 21
CONECT 24 20 25
CONECT 25 11 15 24
CONECT 26 6 27 31 28
CONECT 27 26
CONECT 28 9 26 30 29
CONECT 29 28
CONECT 30 28
CONECT 31 26 34
CONECT 32 1
CONECT 33 1
CONECT 34 31
CONECT 2797 2798
CONECT 2798 2799 2801 2800 2797
CONECT 2799 2798
CONECT 2800 2798
CONECT 2801 2798 2802
CONECT 2802 2801 2804 2805 2803
CONECT 2803 2802
CONECT 2804 2802
CONECT 2805 2802 2806 2807 2824
CONECT 2806 2805
CONECT 2807 2805 2808
CONECT 2808 2807 2826 2809 2810
CONECT 2809 2808
CONECT 2810 2808 2822 2811
CONECT 2811 2810 2813 2812
CONECT 2812 2811
CONECT 2813 2811 2814 2818
CONECT 2814 2813 2815 2817 2816
CONECT 2815 2814
CONECT 2816 2814
CONECT 2817 2814
CONECT 2818 2813 2819 2820
CONECT 2819 2818
CONECT 2820 2818 2821 2822
CONECT 2821 2820
CONECT 2822 2810 2820 2823
CONECT 2823 2822
CONECT 2824 2805 2825 2829 2826
CONECT 2825 2824
CONECT 2826 2808 2824 2827 2828
CONECT 2827 2826
CONECT 2828 2826
CONECT 2829 2824 1
CONECT 2831 2832 5650 2861 2862
CONECT 2832 2831 2833
CONECT 2833 2832 2835 2834 2836
CONECT 2834 2833
CONECT 2835 2833
CONECT 2836 2833 2837 2838 2855
CONECT 2837 2836
CONECT 2838 2836 2839
CONECT 2839 2838 2841 2840 2857
CONECT 2840 2839
CONECT 2841 2839 2854 2842
CONECT 2842 2841 2843 2844
CONECT 2843 2842
CONECT 2844 2842 2845
CONECT 2845 2844 2854 2846
CONECT 2846 2845 2847 2850
CONECT 2847 2846 2849 2848
CONECT 2848 2847
CONECT 2849 2847
CONECT 2850 2846 2851
CONECT 2851 2850 2852 2853
CONECT 2852 2851
CONECT 2853 2851 2854
CONECT 2854 2841 2845 2853
CONECT 2855 2836 2857 2860 2856
CONECT 2856 2855
CONECT 2857 2839 2855 2858 2859
CONECT 2858 2857
CONECT 2859 2857
CONECT 2860 2855 2863
CONECT 2861 2831
CONECT 2862 2831
CONECT 2863 2860
CONECT 5620 5621
CONECT 5621 5623 5624 5622 5620
CONECT 5622 5621
CONECT 5623 5621
CONECT 5624 5621 5625
CONECT 5625 5624 5628 5626 5627
CONECT 5626 5625
CONECT 5627 5625
CONECT 5628 5625 5630 5629 5645
CONECT 5629 5628
CONECT 5630 5628 5631
CONECT 5631 5630 5633 5632 5647
CONECT 5632 5631
CONECT 5633 5631 5643 5634
CONECT 5634 5633 5635 5636
CONECT 5635 5634
CONECT 5636 5634 5637 5638
CONECT 5637 5636
CONECT 5638 5636 5639 5642
CONECT 5639 5638 5640 5641
CONECT 5640 5639
CONECT 5641 5639
CONECT 5642 5638 5643
CONECT 5643 5633 5642 5644
CONECT 5644 5643
CONECT 5645 5628 5646 5650 5647
CONECT 5646 5645
CONECT 5647 5631 5645 5648 5649
CONECT 5648 5647
CONECT 5649 5647
CONECT 5650 5645 2831
END
it is the error:
GROMACS: gmx pdb2gmx, version 2018.4
Executable: /home/fatemeh3/miniconda3/envs/gromacs2018/bin/gmx
Data prefix: /home/fatemeh3/miniconda3/envs/gromacs2018
Working dir: /home/fatemeh3/fatima/CUFIX_bsc0/89
Command line:
gmx pdb2gmx -f str_89_P_dsv_last_1_chimera.pdb
Select the Force Field:
From current directory:
1: AMBER99SB-ildn-phi-bsc0-cufix (Jejoong Yoo and Aleksei Aksimentiev, JCTC 2016, 12, 430–443)
From ‘/home/fatemeh3/miniconda3/envs/gromacs2018/share/gromacs/top’:
2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1
Using the Amber99sb-ildn-phi-bsc0-cufix force field in directory ./amber99sb-ildn-phi-bsc0-cufix.ff
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/watermodels.dat
Select the Water Model:
1: TIP3P TIP 3-point, recommended
2: TIP4P TIP 4-point
3: TIP4P-Ew TIP 4-point optimized with Ewald
4: SPC simple point charge
5: SPC/E extended simple point charge
6: tip4p2005 TIP 4-point optimized in 2005
7: None
1
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/aminoacids.r2b
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/dna.r2b
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/rna.r2b
Reading str_89_P_dsv_last_1_chimera.pdb…
WARNING: all CONECT records are ignored
Read 5649 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 178 residues with 5649 atoms
chain #res #atoms
1 ’ ’ 89 2829
2 ’ ’ 89 2820
All occupancies are one
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/atomtypes.atp
Atomtype 78
Reading residue database… (amber99sb-ildn-phi-bsc0-cufix)
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/aminoacids.rtp
Residue 112
Sorting it all out…
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/dna.rtp
Residue 137
Sorting it all out…
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/rna.rtp
Residue 153
Sorting it all out…
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/aminoacids.hdb
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/dna.hdb
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/rna.hdb
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/aminoacids.n.tdb
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.16#
Processing chain 1 (2829 atoms, 89 residues)
Identified residue DG1 as a starting terminus.
Identified residue DT89 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/aminoacids.arn
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/dna.arn
Opening force field file ./amber99sb-ildn-phi-bsc0-cufix.ff/rna.arn
Program: gmx pdb2gmx, version 2018.4
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)
Fatal error:
Atom P in residue DG 1 was not found in rtp entry DG5 with 31 atoms
while sorting atoms.