bharat gupta wrote:
Sorry to ask this , but what could be done as I don't understand how
could have happened??
I'll assume that you processed your .pdb file with pdb2gmx to get the protein
coordinates in .gro format, but I don't know how you added the ligand
coordinates to the .gro file. If you did it by hand (i.e. copy/paste with a
text editor), then you didn't preserve the required units. If you used some
other program (i.e. editconf) and it did not perform as expected, that is a
separate issue. Since I'm left to guess (you still haven't described exactly
what you've done to construct the file), that's all I can offer.
-Justin
On Fri, Dec 2, 2011 at 11:24 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
bharat gupta wrote:
Here's the coordinate of the phosphate ion from the docked
complex :-
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
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
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
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
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
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
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
ATOM 2230 HG1 THR A 230 -12.152 75.322 5.914 1.00
0.00 0.210 HD
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
HETATM 3 O2 PO4 A 322 27.419 81.238 1.254 1.00
4.49 -0.609 OA
HETATM 4 O3 PO4 A 322 28.535 83.301 0.471 1.00
2.00 -0.609 OA
HETATM 5 O4 PO4 A 322 29.451 82.186 2.489 1.00
4.00 -0.609 OA
Here's the coordinates of the processed file after adding ligand
coordinates :-
230THR N 3601 -1.031 7.389 0.410
230THR HN 3602 -1.054 7.486 0.396
230THR CA 3603 -1.113 7.308 0.502
230THR HA 3604 -1.063 7.222 0.502
230THR CB 3605 -1.118 7.371 0.646
230THR HB 3606 -1.197 7.338 0.697
230THR OG1 3607 -1.135 7.514 0.638
230THR HG1 3608 -1.138 7.552 0.731
230THR CG2 3609 -0.988 7.341 0.722
230THR HG21 3610 -0.993 7.382 0.813
230THR HG22 3611 -0.976 7.242 0.730
230THR HG23 3612 -0.910 7.380 0.672
230THR C 3613 -1.255 7.279 0.449
230THR OT1 3614 -1.294 7.160 0.452
230THR OT2 3615 -1.337 7.205 0.529
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
5.23907 4.16174 3.66560
Your PO4 coordinates are still in Angstrom. They should be nm for a
.gro file.
-Justin
On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
bharat gupta wrote:
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 ??
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.
-Justin
-- ==============================____==========
Justin A. Lemkul
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Room No. : 7202A, 2nd Floor
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==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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