<div dir="ltr">change the string 'HEM' to 'HEME' in <a href="http://HEME.gro">HEME.gro</a> file<br>
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</div><div class="wps_signature" dir="auto"></div><div class="wps_quotion">在 Mehreen Jan <mehreen_jan1990@yahoo.com>，2017年2月10日 12:15写道：<br type='attribution'><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p/><p dir="ltr">hello every one <br>
i want to simulate HEME using gromacs 5.0.7 ff43A1 . i read some where HEME is already present in almost all gromacs FF. when i run Pdb2gmx.......<a href="http://HEME.gro">HEME.gro</a> i got error Residue 'HEM' not found in residue topology database. i compare my PDB with rtp file ... i am shocked to see that my PDB HEM and rtp [HEME] are completely different. i have no idea what to do and how to do?? <br>
i have no access to CHARMM-GUI, SwissParam give me error and ATB didnot provide login password. if some one have HEM modified topology kindly upload it or send. <br>
<br>
my HEME: <br>
<br>
HETATM 1 FE HEM C<a href="tel:1542">1542</a> <a href="tel:732080715">7.320 80.715</a> -<a href="tel:59551002563">5.955 1.00 25.63</a> Fe <br>
HETATM 2 CHA HEM C<a href="tel:1542">1542</a> <a href="tel:782877591">7.828 77.591</a> -<a href="tel:50471002339">5.047 1.00 23.39</a> C <br>
HETATM 3 CHB HEM C<a href="tel:1542">1542</a> <a href="tel:650181578">6.501 81.578</a> -<a href="tel:27331002347">2.733 1.00 23.47</a> C <br>
HETATM 4 CHC HEM C<a href="tel:1542">1542</a> <a href="tel:679884039">6.798 84.039</a> -<a href="tel:68861002200">6.886 1.00 22.00</a> C <br>
HETATM 5 CHD HEM C<a href="tel:1542">1542</a> <a href="tel:741579872">7.415 79.872</a> -<a href="tel:92751002035">9.275 1.00 20.35</a> C <br>
HETATM 6 NA HEM C<a href="tel:1542">1542</a> <a href="tel:723279764">7.232 79.764</a> -<a href="tel:41941002504">4.194 1.00 25.04</a> N <br>
HETATM 7 C1A HEM C<a href="tel:1542">1542</a> <a href="tel:746978413">7.469 78.413</a> -<a href="tel:39801002577">3.980 1.00 25.77</a> C <br>
HETATM 8 C2A HEM C<a href="tel:1542">1542</a> <a href="tel:723678109">7.236 78.109</a> -<a href="tel:26021002675">2.602 1.00 26.75</a> C <br>
HETATM 9 C3A HEM C<a href="tel:1542">1542</a> <a href="tel:684179239">6.841 79.239</a> -<a href="tel:19711002616">1.971 1.00 26.16</a> C <br>
HETATM 10 C4A HEM C<a href="tel:1542">1542</a> <a href="tel:684580286">6.845 80.286</a> -<a href="tel:29561002477">2.956 1.00 24.77</a> C <br>
HETATM 11 CMA HEM C<a href="tel:1542">1542</a> <a href="tel:651279509">6.512 79.509</a> -<a href="tel:04871002324">0.487 1.00 23.24</a> C <br>
HETATM 12 CAA HEM C<a href="tel:1542">1542</a> <a href="tel:738976695">7.389 76.695</a> -<a href="tel:19901003057">1.990 1.00 30.57</a> C <br>
HETATM 13 CBA HEM C<a href="tel:1542">1542</a> <a href="tel:874976200">8.749 76.200</a> -<a href="tel:15031003482">1.503 1.00 34.82</a> C <br>
HETATM 14 CGA HEM C<a href="tel:1542">1542</a> <a href="tel:882774825">8.827 74.825</a> -<a href="tel:08431003787">0.843 1.00 37.87</a> C <br>
HETATM 15 O1A HEM C<a href="tel:1542">1542</a> <a href="tel:793473913">7.934 73.913</a> -<a href="tel:06801003974">0.680 1.00 39.74</a> O <br>
HETATM 16 O2A HEM C<a href="tel:1542">1542</a> <a href="tel:1002174626">10.021 74.626</a> -<a href="tel:04231004042">0.423 1.00 40.42</a> O <br>
HETATM 17 NB HEM C<a href="tel:1542">1542</a> <a href="tel:675182455">6.751 82.455</a> -<a href="tel:49981002310">4.998 1.00 23.10</a> N <br>
HETATM 18 C1B HEM C<a href="tel:1542">1542</a> <a href="tel:646082611">6.460 82.611</a> -<a href="tel:36601002237">3.660 1.00 22.37</a> C <br>
HETATM 19 C2B HEM C<a href="tel:1542">1542</a> <a href="tel:613183997">6.131 83.997</a> -<a href="tel:33671002140">3.367 1.00 21.40</a> C <br>
HETATM 20 C3B HEM C<a href="tel:1542">1542</a> <a href="tel:623584681">6.235 84.681</a> -<a href="tel:45101002171">4.510 1.00 21.71</a> C <br>
HETATM 21 C4B HEM C<a href="tel:1542">1542</a> <a href="tel:661483714">6.614 83.714</a> -<a href="tel:55441002185">5.544 1.00 21.85</a> C <br>
HETATM 22 CMB HEM C<a href="tel:1542">1542</a> <a href="tel:583084540">5.830 84.540</a> -<a href="tel:19471002077">1.947 1.00 20.77</a> C <br>
HETATM 23 CAB HEM C<a href="tel:1542">1542</a> <a href="tel:600986177">6.009 86.177</a> -<a href="tel:48171002085">4.817 1.00 20.85</a> C <br>
HETATM 24 CBB HEM C<a href="tel:1542">1542</a> <a href="tel:489486822">4.894 86.822</a> -<a href="tel:43911002193">4.391 1.00 21.93</a> C <br>
HETATM 25 NC HEM C<a href="tel:1542">1542</a> <a href="tel:718081751">7.180 81.751</a> -<a href="tel:77171002307">7.717 1.00 23.07</a> N <br>
HETATM 26 C1C HEM C<a href="tel:1542">1542</a> <a href="tel:685983099">6.859 83.099</a> -<a href="tel:79101002116">7.910 1.00 21.16</a> C <br>
HETATM 27 C2C HEM C<a href="tel:1542">1542</a> <a href="tel:655983360">6.559 83.360</a> -<a href="tel:93011001955">9.301 1.00 19.55</a> C <br>
HETATM 28 C3C HEM C<a href="tel:1542">1542</a> <a href="tel:672482197">6.724 82.197</a> -<a href="tel:99671001924">9.967 1.00 19.24</a> C <br>
HETATM 29 C4C HEM C<a href="tel:1542">1542</a> <a href="tel:713281190">7.132 81.190</a> -<a href="tel:90231002112">9.023 1.00 21.12</a> C <br>
HETATM 30 CMC HEM C<a href="tel:1542">1542</a> <a href="tel:611984748">6.119 84.748</a> -<a href="tel:98151001745">9.815 1.00 17.45</a> C <br>
HETATM 31 CAC HEM C<a href="tel:1542">1542</a> <a href="tel:650681891">6.506 81.891</a> -<a href="tel:114551001762">11.455 1.00 17.62</a> C <br>
HETATM 32 CBC HEM C<a href="tel:1542">1542</a> <a href="tel:561682527">5.616 82.527</a> -<a href="tel:122361001811">12.236 1.00 18.11</a> C <br>
HETATM 33 ND HEM C<a href="tel:1542">1542</a> <a href="tel:759379010">7.593 79.010</a> -<a href="tel:69811002241">6.981 1.00 22.41</a> N <br>
HETATM 34 C1D HEM C<a href="tel:1542">1542</a> <a href="tel:763578876">7.635 78.876</a> -<a href="tel:83521002108">8.352 1.00 21.08</a> C <br>
HETATM 35 C2D HEM C<a href="tel:1542">1542</a> <a href="tel:783577476">7.835 77.476</a> -<a href="tel:86541002166">8.654 1.00 21.66</a> C <br>
HETATM 36 C3D HEM C<a href="tel:1542">1542</a> <a href="tel:791376830">7.913 76.830</a> -<a href="tel:75051002101">7.505 1.00 21.01</a> C <br>
HETATM 37 C4D HEM C<a href="tel:1542">1542</a> <a href="tel:776377760">7.763 77.760</a> -<a href="tel:64231002207">6.423 1.00 22.07</a> C <br>
HETATM 38 CMD HEM C<a href="tel:1542">1542</a> <a href="tel:791976887">7.919 76.887</a> -<a href="tel:101021002029">10.102 1.00 20.29</a> C <br>
HETATM 39 CAD HEM C<a href="tel:1542">1542</a> <a href="tel:813175321">8.131 75.321</a> -<a href="tel:73211002098">7.321 1.00 20.98</a> C <br>
HETATM 40 CBD HEM C<a href="tel:1542">1542</a> <a href="tel:672374752">6.723 74.752</a> -<a href="tel:70271002317">7.027 1.00 23.17</a> C <br>
HETATM 41 CGD HEM C<a href="tel:1542">1542</a> <a href="tel:676873298">6.768 73.298</a> -<a href="tel:67941002491">6.794 1.00 24.91</a> C <br>
HETATM 42 O1D HEM C<a href="tel:1542">1542</a> <a href="tel:624272753">6.242 72.753</a> -<a href="tel:58081002944">5.808 1.00 29.44</a> O <br>
HETATM 43 O2D HEM C<a href="tel:1542">1542</a> <a href="tel:740672657">7.406 72.657</a> -<a href="tel:76301002684">7.630 1.00 26.84</a> O <br>
HETATM 44 HHA HEM C<a href="tel:1542">1542</a> <a href="tel:823676638">8.236 76.638</a> -<a href="tel:4744100000">4.744 1.00 0.00</a> H <br>
HETATM 45 HHB HEM C<a href="tel:1542">1542</a> <a href="tel:622881833">6.228 81.833</a> -<a href="tel:1720100000">1.720 1.00 0.00</a> H <br>
HETATM 46 HHC HEM C<a href="tel:1542">1542</a> <a href="tel:689985082">6.899 85.082</a> -<a href="tel:7147100000">7.147 1.00 0.00</a> H <br>
HETATM 47 HHD HEM C<a href="tel:1542">1542</a> <a href="tel:747179584">7.471 79.584</a> -<a href="tel:10314100000">10.314 1.00 0.00</a> H <br>
HETATM 48 HMA1 HEM C<a href="tel:1542">1542</a> <a href="tel:555979043">5.559 79.043</a> -<a href="tel:0235100000">0.235 1.00 0.00</a> H <br>
HETATM 49 HMA2 HEM C<a href="tel:1542">1542</a> 7.<a href="tel:29879">298 79</a>.<a href="tel:0910141100000">091 0.141 1.00 0.00</a> H <br>
HETATM 50 HMA3 HEM C<a href="tel:1542">1542</a> <a href="tel:644680584">6.446 80.584</a> -<a href="tel:0319100000">0.319 1.00 0.00</a> H <br>
HETATM 51 HAA2 HEM C<a href="tel:1542">1542</a> <a href="tel:705575989">7.055 75.989</a> -<a href="tel:2750100000">2.750 1.00 0.00</a> H <br>
HETATM 52 HAA3 HEM C<a href="tel:1542">1542</a> <a href="tel:669676625">6.696 76.625</a> -<a href="tel:1151100000">1.151 1.00 0.00</a> H <br>
HETATM 53 HBA2 HEM C<a href="tel:1542">1542</a> <a href="tel:941376181">9.413 76.181</a> -<a href="tel:2367100000">2.367 1.00 0.00</a> H <br>
HETATM 54 HBA3 HEM C<a href="tel:1542">1542</a> <a href="tel:913976933">9.139 76.933</a> -<a href="tel:0797100000">0.797 1.00 0.00</a> H <br>
HETATM 55 HMB1 HEM C<a href="tel:1542">1542</a> <a href="tel:675484582">6.754 84.582</a> -<a href="tel:1370100000">1.370 1.00 0.00</a> H <br>
HETATM 56 HMB2 HEM C<a href="tel:1542">1542</a> <a href="tel:540485541">5.404 85.541</a> -<a href="tel:2024100000">2.024 1.00 0.00</a> H <br>
HETATM 57 HMB3 HEM C<a href="tel:1542">1542</a> <a href="tel:512083880">5.120 83.880</a> -<a href="tel:1449100000">1.449 1.00 0.00</a> H <br>
HETATM 58 HAB HEM C<a href="tel:1542">1542</a> <a href="tel:675286720">6.752 86.720</a> -<a href="tel:5381100000">5.381 1.00 0.00</a> H <br>
HETATM 59 HBB1 HEM C<a href="tel:1542">1542</a> <a href="tel:414486288">4.144 86.288</a> -<a href="tel:3826100000">3.826 1.00 0.00</a> H <br>
HETATM 60 HBB2 HEM C<a href="tel:1542">1542</a> <a href="tel:475687869">4.756 87.869</a> -<a href="tel:4617100000">4.617 1.00 0.00</a> H <br>
HETATM 61 HMC1 HEM C<a href="tel:1542">1542</a> <a href="tel:682185505">6.821 85.505</a> -<a href="tel:9465100000">9.465 1.00 0.00</a> H <br>
HETATM 62 HMC2 HEM C<a href="tel:1542">1542</a> <a href="tel:610384743">6.103 84.743</a> -<a href="tel:10905100000">10.905 1.00 0.00</a> H <br>
HETATM 63 HMC3 HEM C<a href="tel:1542">1542</a> <a href="tel:512284976">5.122 84.976</a> -<a href="tel:9438100000">9.438 1.00 0.00</a> H <br>
HETATM 64 HAC HEM C<a href="tel:1542">1542</a> <a href="tel:710781114">7.107 81.114</a> -<a href="tel:11904100000">11.904 1.00 0.00</a> H <br>
HETATM 65 HBC1 HEM C<a href="tel:1542">1542</a> <a href="tel:499783310">4.997 83.310</a> -<a href="tel:11823100000">11.823 1.00 0.00</a> H <br>
HETATM 66 HBC2 HEM C<a href="tel:1542">1542</a> <a href="tel:552082255">5.520 82.255</a> -<a href="tel:13277100000">13.277 1.00 0.00</a> H <br>
HETATM 67 HMD1 HEM C<a href="tel:1542">1542</a> <a href="tel:831775873">8.317 75.873</a> -<a href="tel:10060100000">10.060 1.00 0.00</a> H <br>
HETATM 68 HMD2 HEM C<a href="tel:1542">1542</a> <a href="tel:692376868">6.923 76.868</a> -<a href="tel:10545100000">10.545 1.00 0.00</a> H <br>
HETATM 69 HMD3 HEM C<a href="tel:1542">1542</a> <a href="tel:857577510">8.575 77.510</a> -<a href="tel:10710100000">10.710 1.00 0.00</a> H <br>
HETATM 70 HAD2 HEM C<a href="tel:1542">1542</a> <a href="tel:854274879">8.542 74.879</a> -<a href="tel:8229100000">8.229 1.00 0.00</a> H <br>
HETATM 71 HAD3 HEM C<a href="tel:1542">1542</a> <a href="tel:879675136">8.796 75.136</a> -<a href="tel:6477100000">6.477 1.00 0.00</a> H <br>
HETATM 72 HBD2 HEM C<a href="tel:1542">1542</a> <a href="tel:607474954">6.074 74.954</a> -<a href="tel:7879100000">7.879 1.00 0.00</a> H <br>
HETATM 73 HBD3 HEM C<a href="tel:1542">1542</a> <a href="tel:631675243">6.316 75.243</a> -<a href="tel:6143100000">6.143 1.00 0.00</a> H <br>
END <br>
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