Here's the coordinate of the phosphate ion from the docked complex :-<div><div>ATOM 2209 N GLY A 228 -4.491 73.252 3.100 1.00 31.50 -0.336 N </div><div>ATOM 2210 HN GLY A 228 -4.765 72.618 3.850 1.00 0.00 0.164 HD</div>
<div>ATOM 2211 CA GLY A 228 -4.817 74.668 3.205 1.00 34.50 0.189 C </div><div>ATOM 2212 C GLY A 228 -6.283 75.040 3.026 1.00 36.60 0.253 C </div><div>ATOM 2213 O GLY A 228 -6.638 76.216 3.151 1.00 36.80 -0.270 OA</div>
<div>ATOM 2214 N ILE A 229 -7.109 74.064 2.647 1.00 38.60 -0.337 N </div><div>ATOM 2215 HN ILE A 229 -6.718 73.136 2.484 1.00 0.00 0.164 HD</div><div>ATOM 2216 CA ILE A 229 -8.556 74.256 2.452 1.00 41.10 0.159 C </div>
<div>ATOM 2217 C ILE A 229 -9.275 73.368 3.447 1.00 43.10 0.251 C </div><div>ATOM 2218 O ILE A 229 -8.856 72.229 3.655 1.00 43.60 -0.271 OA</div><div>ATOM 2219 CB ILE A 229 -9.003 73.826 1.031 1.00 40.40 0.029 C </div>
<div>ATOM 2220 CG1 ILE A 229 -8.528 74.844 0.013 1.00 40.50 0.002 C </div><div>ATOM 2221 CG2 ILE A 229 -10.512 73.689 0.942 1.00 39.90 0.002 C </div><div>ATOM 2222 CD1 ILE A 229 -8.610 74.327 -1.389 1.00 41.40 0.000 C </div>
<div>ATOM 2223 N THR A 230 -10.312 73.894 4.098 1.00 45.60 -0.337 N </div><div>ATOM 2224 HN THR A 230 -10.544 74.877 3.957 1.00 0.00 0.164 HD</div><div>ATOM 2225 CA THR A 230 -11.129 73.085 5.017 1.00 47.90 0.172 C </div>
<div>ATOM 2226 C THR A 230 -12.555 72.789 4.490 1.00 49.10 0.232 C </div><div>ATOM 2227 O THR A 230 -12.945 71.602 4.523 1.00 50.90 -0.286 OA</div><div>ATOM 2228 CB THR A 230 -11.179 73.714 6.460 1.00 48.20 0.139 C </div>
<div>ATOM 2229 OG1 THR A 230 -11.348 75.136 6.384 1.00 48.60 -0.383 OA</div><div>ATOM 2230 HG1 THR A 230 -12.152 75.322 5.914 1.00 0.00 0.210 HD</div><div>ATOM 2231 CG2 THR A 230 -9.880 73.414 7.220 1.00 49.10 0.034 C </div>
<div>TER 2232 THR A 230 </div><div>HETATM 1 P PO4 A 322 28.148 82.525 1.696 1.00 2.95 0.437 P </div><div>HETATM 2 O1 PO4 A 322 27.246 83.314 2.595 1.00 5.93 -0.609 OA</div><div>
HETATM 3 O2 PO4 A 322 27.419 81.238 1.254 1.00 4.49 -0.609 OA</div><div>HETATM 4 O3 PO4 A 322 28.535 83.301 0.471 1.00 2.00 -0.609 OA</div><div>HETATM 5 O4 PO4 A 322 29.451 82.186 2.489 1.00 4.00 -0.609 OA</div>
<div><br></div><div><br></div><div><br></div><div>Here's the coordinates of the processed file after adding ligand coordinates :-</div><div><br></div><div><br></div><div><span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR N 3601 -1.031 7.389 0.410</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR HN 3602 -1.054 7.486 0.396</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR CA 3603 -1.113 7.308 0.502</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR HA 3604 -1.063 7.222 0.502</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR CB 3605 -1.118 7.371 0.646</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR HB 3606 -1.197 7.338 0.697</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR OG1 3607 -1.135 7.514 0.638</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR HG1 3608 -1.138 7.552 0.731</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR CG2 3609 -0.988 7.341 0.722</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR HG21 3610 -0.993 7.382 0.813</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR HG22 3611 -0.976 7.242 0.730</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR HG23 3612 -0.910 7.380 0.672</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR C 3613 -1.255 7.279 0.449</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR OT1 3614 -1.294 7.160 0.452</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 230THR OT2 3615 -1.337 7.205 0.529</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 1LIG P 1 28.261 82.425 1.961 </span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 1LIG O1 2 27.805 80.999 1.894 </span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 1LIG O2 3 28.523 82.938 0.528 </span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 1LIG O3 4 27.235 83.311 2.606 </span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 1LIG O4 5 29.563 82.481 2.823</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "> 5.23907 4.16174 3.66560</span></div><div><br></div><br>
<div class="gmail_quote">On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><br>
<br>
bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I checked the docked structure and the structure obtained after adding the ligand coordinates to the processed file obtained after using pdb2gmx command. It's very surprising that in the docked structure ligand is at the correct place but the processed gromacs file the ligand lies far apart from the protein. Any clue what could be the reason for this ??<br>
<br>
</blockquote>
<br></div>
If the docked structure is correct, and the one you reassembled is incorrect, you made some mistake in putting it back together. It's impossible to say what went wrong based on the (lack of) information given.<span><font color="#888888"><br>
<br>
-Justin</font></span><div><div><br>
<br>
-- <br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div>
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