<span lang="EN">
<p>Hi all.</p>
<p>I'm working with gromacs 4.0.5 in amber99 force field. I have two questions:</p>
<p>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?</p>
<p>2. One of the goals of my work is studing of aminoacyl-adenylat behavior:</p>
<p>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:</p>
<font size="3" face="Courier New"><font size="3" face="Courier New">
<p>a)[ RA3 ]</p>
<p>[ atoms ]</p>
<p>N amber99_39 0.05770 1</p>
<p>H9 amber99_24 0.22720 2</p>
<p>CA amber99_11 -0.00540 3</p>
<p>HA amber99_28 0.10930 4</p>
<p>CB amber99_11 0.31960 5</p>
<p>HB amber99_18 -0.02210 6</p>
<p>CG1 amber99_11 -0.31290 7</p>
<p>HG11 amber99_18 0.07350 8</p>
<p>HG12 amber99_18 0.07350 9</p>
<p>HG13 amber99_18 0.07350 10</p>
<p>CG2 amber99_11 -0.31290 11</p>
<p>HG21 amber99_18 0.07350 12</p>
<p>HG22 amber99_18 0.07350 13</p>
<p>HG23 amber99_18 0.07350 14</p>
<p>C amber99_2 0.61630 15</p>
<p>O amber99_41 -0.57220 16 </p>
<p>P amber99_46 1.16620 17</p>
<p>O1P amber99_45 -0.77600 18</p>
<p>O2P amber99_45 -0.77600 19</p>
<p>O5' amber99_44 -0.49890 20</p>
<p>C5' amber99_11 0.05580 21</p>
<p>H5'1 amber99_19 0.06790 22</p>
<p>H5'2 amber99_19 0.06790 23</p>
<p>C4' amber99_11 0.10650 24</p>
<p>H4' amber99_19 0.11740 25</p>
<p>O4' amber99_44 -0.35480 26</p>
<p>C1' amber99_11 0.03940 27</p>
<p>H1' amber99_20 0.20070 28</p>
<p>N9 amber99_40 -0.02510 29</p>
<p>C8 amber99_6 0.20060 30</p>
<p>H8 amber99_24 0.15530 31</p>
<p>N7 amber99_36 -0.60730 32</p>
<p>C5 amber99_4 0.05150 33</p>
<p>C6 amber99_3 0.70090 34</p>
<p>N6 amber99_38 -0.90190 35</p>
<p>H61 amber99_17 0.41150 36</p>
<p>H62 amber99_17 0.41150 37</p>
<p>N1 amber99_37 -0.76150 38</p>
<p>C2 amber99_9 0.58750 39</p>
<p>N3 amber99_37 -0.69970 40</p>
<p>C4 amber99_4 0.30530 41</p>
<p>C3' amber99_11 0.20220 42</p>
<p>H3' amber99_19 0.06150 43</p>
<p>C2' amber99_11 0.06700 44</p>
<p>H2'1 amber99_19 0.09720 45</p>
<p>O2' amber99_44 -0.61390 46</p>
<p>HO'2 amber99_25 0.41860 47</p>
<p>O3' amber99_43 -0.65410 48</p>
<p>H1 amber99_17 0.22720 49</p>
<p>H2 amber99_17 0.22720 50</p>
<p>H3 amber99_17 0.22720 51 </p>
<p>[ bonds ]</p>
<p>P O1P</p>
<p>P O2P</p>
<p>P O5'</p>
<p>O5' C5'</p>
<p>C5' H5'1</p>
<p>C5' H5'2</p>
<p>C5' C4'</p>
<p>C4' H4'</p>
<p>C4' O4'</p>
<p>C4' C3'</p>
<p>O4' C1'</p>
<p>C1' H1'</p>
<p>C1' N9</p>
<p>C1' C2'</p>
<p>N9 C8</p>
<p>N9 C4</p>
<p>C8 H8</p>
<p>C8 N7</p>
<p>N7 C5</p>
<p>C5 C6</p>
<p>C5 C4</p>
<p>C6 N6</p>
<p>C6 N1</p>
<p>N6 H61</p>
<p>N6 H62</p>
<p>N1 C2</p>
<p>C2 H9</p>
<p>C2 N3</p>
<p>N3 C4</p>
<p>C3' H3'</p>
<p>C3' C2'</p>
<p>C3' O3'</p>
<p>C2' H2'1</p>
<p>C2' O2'</p>
<p>O3' HO'2</p>
<p>O2' C</p>
<p>-O3' P</p>
<p>N H1</p>
<p>N H2</p>
<p>N H3</p>
<p>N CA</p>
<p>CA HA</p>
<p>CA CB</p>
<p>CA C</p>
<p>CB HB</p>
<p>CB CG1</p>
<p>CB CG2</p>
<p>CG1 HG11</p>
<p>CG1 HG12</p>
<p>CG1 HG13</p>
<p>CG2 HG21</p>
<p>CG2 HG22</p>
<p>CG2 HG23</p>
<p>C O</p>
<p>C +N</p>
<p>[ dihedrals ]</p>
<p>O4' C1' N9 C4 proper_X_CT_N*_X </p>
<p>C1' N9 C8 H8 proper_X_CK_N*_X</p>
<p>C1' N9 C8 N7 proper_X_CK_N*_X</p>
<p>C1' N9 C4 C5 proper_X_CB_N*_X</p>
<p>C1' N9 C4 N3 proper_X_CB_N*_X</p>
<p>H1' C1' N9 C8 proper_X_CT_N*_X </p>
<p>H1' C1' N9 C4 proper_X_CT_N*_X</p>
<p>C8 N9 C4 C5 proper_X_CB_N*_X</p>
<p>C8 N9 C4 N3 proper_X_CB_N*_X</p>
<p>C5 C6 N1 C2 proper_X_CA_NC_X</p>
<p>N6 C6 N1 C2 proper_X_CA_NC_X</p>
<p>N1 C2 N3 C4 proper_X_CQ_NC_X</p>
<p>H9 C2 N3 C4 proper_X_CQ_NC_X</p>
<p>H8 C8 N7 C5 proper_X_CK_NB_X</p>
<p>N9 C8 N7 C5 proper_X_CK_NB_X</p>
<p>H62 N6 C6 N1 proper_X_CA_N2_X</p>
<p>H61 N6 C6 N1 proper_X_CA_N2_X</p>
<p>C5 C6 N6 H61 proper_X_CA_N2_X</p>
<p>C5 C6 N6 H62 proper_X_CA_N2_X</p>
<p>H8 C8 N9 C4 proper_X_CK_N*_X</p>
<p>N7 C8 N9 C4 proper_X_CK_N*_X</p>
<p>O5' C5' C4' H4' proper_H_CT_CT_O</p>
<p>H5'1 C5' C4' O4' proper_H_CT_CT_O</p>
<p>H5'2 C5' C4' O4' proper_H_CT_CT_O</p>
<p>O4' C4' C3' H3' proper_H_CT_CT_O</p>
<p>O4' C1' C2' H2'1 proper_H_CT_CT_O</p>
<p>C2' O2' C CA proper_H_CT_CT_O</p>
<p>CA C +N +H backbone_prop_1</p>
<p>O C +N +H backbone_prop_2</p>
<p>CA C +N +CA backbone_prop_1</p>
<p>O C +N +CA backbone_prop_1</p>
<p>[ impropers ]</p>
<p>C4 C8 N9 C1' nucleic_imp_10</p>
<p>C6 H61 N6 H62</p>
<p>N9 N7 C8 H8</p>
<p>N1 N3 C2 H9 nucleic_imp_11</p>
<p>C5 N6 C6 N1 nucleic_imp_11</p>
<p>CA +N C O</p>
<p>b)RA3 14</p>
<p>2 6 H5' C5' O5' C4' </p>
<p>1 5 H4' C4' C5' O4' C3' </p>
<p>1 5 H1' C1' O4' N9 C2' </p>
<p>1 1 H8 C8 N9 N7 </p>
<p>2 3 H6 N6 C6 C5 </p>
<p>1 1 H9 C2 N1 N3 </p>
<p>1 5 H3' C3' C4' C2' O3' </p>
<p>1 5 H2'1 C2' C1' C3' O2' </p>
<p>1 2 HO'2 O3' C3' C4' </p>
<p>3 4 H N CA CB </p>
<p>1 5 HA CA N CB C </p>
<p>1 5 HB CB CA CG1 CG2 </p>
<p>3 4 HG1 CG1 CB CA </p>
<p>3 4 HG2 CG2 CB CA</p>
<p>c)CT OS C 1 109.500 502.080 ; </p></font></font><font size="3">
<p>(</p></font><font size="3" face="Courier New"><font size="3" face="Courier New">amber99_11 12.01000 ; CT sp3 aliphatic C/
<p>amber99_44 16.00000 ; OS ether and ester oxygen/</p>
<p>amber99_2 12.01000 ; C sp2 C carbonyl group/)</p></font></font><font size="3">
<p>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 </p>
</font></span><font size="3" face="Calibri"><font size="3" face="Calibri"><span lang="RU">№</span></font></font><font size="3"><span lang="EN"> !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
<p>Source code file: pgutil.c, line: 87</p>
<p>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...</p>
<div>Please, help me.</div>
<div>thanks</div></span></font>