Sorry to ask this , but what could be done as I don't understand how could have happened??<br><br><div class="gmail_quote">On Fri, Dec 2, 2011 at 11:24 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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 class="HOEnZb"><div class="h5"><br>
<br>
bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Here's the coordinate of the phosphate ion from the docked complex :-<br>
ATOM 2209 N GLY A 228 -4.491 73.252 3.100 1.00 31.50 -0.336 N ATOM 2210 HN GLY A 228 -4.765 72.618 3.850 1.00 0.00 0.164 HD<br>
ATOM 2211 CA GLY A 228 -4.817 74.668 3.205 1.00 34.50 0.189 C ATOM 2212 C GLY A 228 -6.283 75.040 3.026 1.00 36.60 0.253 C ATOM 2213 O GLY A 228 -6.638 76.216 3.151 1.00 36.80 -0.270 OA<br>
ATOM 2214 N ILE A 229 -7.109 74.064 2.647 1.00 38.60 -0.337 N ATOM 2215 HN ILE A 229 -6.718 73.136 2.484 1.00 0.00 0.164 HD<br>
ATOM 2216 CA ILE A 229 -8.556 74.256 2.452 1.00 41.10 0.159 C ATOM 2217 C ILE A 229 -9.275 73.368 3.447 1.00 43.10 0.251 C ATOM 2218 O ILE A 229 -8.856 72.229 3.655 1.00 43.60 -0.271 OA<br>
ATOM 2219 CB ILE A 229 -9.003 73.826 1.031 1.00 40.40 0.029 C ATOM 2220 CG1 ILE A 229 -8.528 74.844 0.013 1.00 40.50 0.002 C ATOM 2221 CG2 ILE A 229 -10.512 73.689 0.942 1.00 39.90 0.002 C ATOM 2222 CD1 ILE A 229 -8.610 74.327 -1.389 1.00 41.40 0.000 C ATOM 2223 N THR A 230 -10.312 73.894 4.098 1.00 45.60 -0.337 N ATOM 2224 HN THR A 230 -10.544 74.877 3.957 1.00 0.00 0.164 HD<br>
ATOM 2225 CA THR A 230 -11.129 73.085 5.017 1.00 47.90 0.172 C ATOM 2226 C THR A 230 -12.555 72.789 4.490 1.00 49.10 0.232 C ATOM 2227 O THR A 230 -12.945 71.602 4.523 1.00 50.90 -0.286 OA<br>
ATOM 2228 CB THR A 230 -11.179 73.714 6.460 1.00 48.20 0.139 C ATOM 2229 OG1 THR A 230 -11.348 75.136 6.384 1.00 48.60 -0.383 OA<br>
ATOM 2230 HG1 THR A 230 -12.152 75.322 5.914 1.00 0.00 0.210 HD<br>
ATOM 2231 CG2 THR A 230 -9.880 73.414 7.220 1.00 49.10 0.034 C TER 2232 THR A 230 HETATM 1 P PO4 A 322 28.148 82.525 1.696 1.00 2.95 0.437 P HETATM 2 O1 PO4 A 322 27.246 83.314 2.595 1.00 5.93 -0.609 OA<br>
HETATM 3 O2 PO4 A 322 27.419 81.238 1.254 1.00 4.49 -0.609 OA<br>
HETATM 4 O3 PO4 A 322 28.535 83.301 0.471 1.00 2.00 -0.609 OA<br>
HETATM 5 O4 PO4 A 322 29.451 82.186 2.489 1.00 4.00 -0.609 OA<br>
<br>
<br>
<br>
Here's the coordinates of the processed file after adding ligand coordinates :-<br>
<br>
<br>
230THR N 3601 -1.031 7.389 0.410<br>
230THR HN 3602 -1.054 7.486 0.396<br>
230THR CA 3603 -1.113 7.308 0.502<br>
230THR HA 3604 -1.063 7.222 0.502<br>
230THR CB 3605 -1.118 7.371 0.646<br>
230THR HB 3606 -1.197 7.338 0.697<br>
230THR OG1 3607 -1.135 7.514 0.638<br>
230THR HG1 3608 -1.138 7.552 0.731<br>
230THR CG2 3609 -0.988 7.341 0.722<br>
230THR HG21 3610 -0.993 7.382 0.813<br>
230THR HG22 3611 -0.976 7.242 0.730<br>
230THR HG23 3612 -0.910 7.380 0.672<br>
230THR C 3613 -1.255 7.279 0.449<br>
230THR OT1 3614 -1.294 7.160 0.452<br>
230THR OT2 3615 -1.337 7.205 0.529<br>
1LIG P 1 28.261 82.425 1.961 1LIG O1 2 27.805 80.999 1.894 1LIG O2 3 28.523 82.938 0.528 1LIG O3 4 27.235 83.311 2.606 1LIG O4 5 29.563 82.481 2.823<br>
5.23907 4.16174 3.66560<br>
<br>
</blockquote>
<br></div></div>
Your PO4 coordinates are still in Angstrom. They should be nm for a .gro file.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
bharat gupta wrote:<br>
<br>
I checked the docked structure and the structure obtained after<br>
adding the ligand coordinates to the processed file obtained<br>
after using pdb2gmx command. It's very surprising that in the<br>
docked structure ligand is at the correct place but the<br>
processed gromacs file the ligand lies far apart from the<br>
protein. Any clue what could be the reason for this ??<br>
<br>
<br>
If the docked structure is correct, and the one you reassembled is<br>
incorrect, you made some mistake in putting it back together. It's<br>
impossible to say what went wrong based on the (lack of) information<br>
given.<br>
<br>
-Justin<br>
<br>
<br></div>
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Justin A. Lemkul<br>
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-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
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</blockquote><div class="HOEnZb"><div class="h5">
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==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<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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