Hi all. I'm working with gromacs 4.0.5 in amber99 force field. I have two questions:
1. The protein part of my complex (trna+protein) consists of 870 aminoacids and two atoms of Zn. The question is - whether I have to create an index file, which will unit aminoacids and Zn in one "protein" or not? If not - whether those Zn will be stable during dynamics or they will escape from the structure in the water? 2. One of the goals of my work is studing of aminoacyl-adenylat behavior: look, when I added aminoacid to adenyn through O2' in hyperchem and then created topology everything was fine untill I get to dynamics (even steep and gradient)... results I saw were very bad, aminoacid flied away from adenyn...I thought gromacs doesn't see this bond between aminoacid and nucleotide...saw I created a new topology for it! It represents both elements (aa and nucleotide) as a one. And I have written a new bond in ff...bon.itp . This is examples of my work - fragments of a) .rtp, b) .hdb, c) ff..bon.itp: a)[ RA3 ] [ atoms ] N amber99_39 0.05770 1 H9 amber99_24 0.22720 2 CA amber99_11 -0.00540 3 HA amber99_28 0.10930 4 CB amber99_11 0.31960 5 HB amber99_18 -0.02210 6 CG1 amber99_11 -0.31290 7 HG11 amber99_18 0.07350 8 HG12 amber99_18 0.07350 9 HG13 amber99_18 0.07350 10 CG2 amber99_11 -0.31290 11 HG21 amber99_18 0.07350 12 HG22 amber99_18 0.07350 13 HG23 amber99_18 0.07350 14 C amber99_2 0.61630 15 O amber99_41 -0.57220 16 P amber99_46 1.16620 17 O1P amber99_45 -0.77600 18 O2P amber99_45 -0.77600 19 O5' amber99_44 -0.49890 20 C5' amber99_11 0.05580 21 H5'1 amber99_19 0.06790 22 H5'2 amber99_19 0.06790 23 C4' amber99_11 0.10650 24 H4' amber99_19 0.11740 25 O4' amber99_44 -0.35480 26 C1' amber99_11 0.03940 27 H1' amber99_20 0.20070 28 N9 amber99_40 -0.02510 29 C8 amber99_6 0.20060 30 H8 amber99_24 0.15530 31 N7 amber99_36 -0.60730 32 C5 amber99_4 0.05150 33 C6 amber99_3 0.70090 34 N6 amber99_38 -0.90190 35 H61 amber99_17 0.41150 36 H62 amber99_17 0.41150 37 N1 amber99_37 -0.76150 38 C2 amber99_9 0.58750 39 N3 amber99_37 -0.69970 40 C4 amber99_4 0.30530 41 C3' amber99_11 0.20220 42 H3' amber99_19 0.06150 43 C2' amber99_11 0.06700 44 H2'1 amber99_19 0.09720 45 O2' amber99_44 -0.61390 46 HO'2 amber99_25 0.41860 47 O3' amber99_43 -0.65410 48 H1 amber99_17 0.22720 49 H2 amber99_17 0.22720 50 H3 amber99_17 0.22720 51 [ bonds ] P O1P P O2P P O5' O5' C5' C5' H5'1 C5' H5'2 C5' C4' C4' H4' C4' O4' C4' C3' O4' C1' C1' H1' C1' N9 C1' C2' N9 C8 N9 C4 C8 H8 C8 N7 N7 C5 C5 C6 C5 C4 C6 N6 C6 N1 N6 H61 N6 H62 N1 C2 C2 H9 C2 N3 N3 C4 C3' H3' C3' C2' C3' O3' C2' H2'1 C2' O2' O3' HO'2 O2' C -O3' P N H1 N H2 N H3 N CA CA HA CA CB CA C CB HB CB CG1 CB CG2 CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 CG2 HG22 CG2 HG23 C O C +N [ dihedrals ] O4' C1' N9 C4 proper_X_CT_N*_X C1' N9 C8 H8 proper_X_CK_N*_X C1' N9 C8 N7 proper_X_CK_N*_X C1' N9 C4 C5 proper_X_CB_N*_X C1' N9 C4 N3 proper_X_CB_N*_X H1' C1' N9 C8 proper_X_CT_N*_X H1' C1' N9 C4 proper_X_CT_N*_X C8 N9 C4 C5 proper_X_CB_N*_X C8 N9 C4 N3 proper_X_CB_N*_X C5 C6 N1 C2 proper_X_CA_NC_X N6 C6 N1 C2 proper_X_CA_NC_X N1 C2 N3 C4 proper_X_CQ_NC_X H9 C2 N3 C4 proper_X_CQ_NC_X H8 C8 N7 C5 proper_X_CK_NB_X N9 C8 N7 C5 proper_X_CK_NB_X H62 N6 C6 N1 proper_X_CA_N2_X H61 N6 C6 N1 proper_X_CA_N2_X C5 C6 N6 H61 proper_X_CA_N2_X C5 C6 N6 H62 proper_X_CA_N2_X H8 C8 N9 C4 proper_X_CK_N*_X N7 C8 N9 C4 proper_X_CK_N*_X O5' C5' C4' H4' proper_H_CT_CT_O H5'1 C5' C4' O4' proper_H_CT_CT_O H5'2 C5' C4' O4' proper_H_CT_CT_O O4' C4' C3' H3' proper_H_CT_CT_O O4' C1' C2' H2'1 proper_H_CT_CT_O C2' O2' C CA proper_H_CT_CT_O CA C +N +H backbone_prop_1 O C +N +H backbone_prop_2 CA C +N +CA backbone_prop_1 O C +N +CA backbone_prop_1 [ impropers ] C4 C8 N9 C1' nucleic_imp_10 C6 H61 N6 H62 N9 N7 C8 H8 N1 N3 C2 H9 nucleic_imp_11 C5 N6 C6 N1 nucleic_imp_11 CA +N C O b)RA3 14 2 6 H5' C5' O5' C4' 1 5 H4' C4' C5' O4' C3' 1 5 H1' C1' O4' N9 C2' 1 1 H8 C8 N9 N7 2 3 H6 N6 C6 C5 1 1 H9 C2 N1 N3 1 5 H3' C3' C4' C2' O3' 1 5 H2'1 C2' C1' C3' O2' 1 2 HO'2 O3' C3' C4' 3 4 H N CA CB 1 5 HA CA N CB C 1 5 HB CB CA CG1 CG2 3 4 HG1 CG1 CB CA 3 4 HG2 CG2 CB CA c)CT OS C 1 109.500 502.080 ; (amber99_11 12.01000 ; CT sp3 aliphatic C/ amber99_44 16.00000 ; OS ether and ester oxygen/ amber99_2 12.01000 ; C sp2 C carbonyl group/) The problem is that, when I tried molecule of aminoacyladenylate in dynamics - everything is ok. But in complex there a lot of warnings and errors with pdb2gmx topology creating. First of all, when I did my first efforts I described above ("when I added aminoacid to adenyn through O2' in hyperchem and then created topology everything was fine untill I get to dynamics") I had atom name O2 in RC and RU (cytozine, uracyl) in pdb file and had no problems, but now gromacs couldn't find it, and I saw that in .rtp it has name "O"...ok, I changed all O2 in cytozynes and uracyls...gromacs is satisfied with but it is an error in aa No. !random acid! it depends on time I run pdb2gmx, every time another atom not found while adding hydrogens. I'm sure that atom names corresponds to each other in pdb and in hdb or rtp base...If I make a little changes in coordinates of this atom - other atom in some acid is bad...and so on, untill I have got an error Source code file: pgutil.c, line: 87 Fatal error: atom N not found in residue -1072258112 while adding impropers (I eve can't find this atom). -missing - is ok. But on the stage of grompp I got an error "no default angle", without any explanations... Please, help me. thanks
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