[gmx-users] Re: Protein ligand simulation
bharat gupta
bharat.85.monu at gmail.com
Fri Dec 2 03:47:15 CET 2011
Yes, I prepared the protein file separately using pdb2gmx and then I pasted
the ligand manually from the docked file.
On Fri, Dec 2, 2011 at 11:44 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 <jalemkul at vt.edu<mailto:
>> jalemkul at 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
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>> 231-9080
>> http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
>> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>> >
>> <http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin
>> <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 : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
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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://vt.edu/Pages/Personal/justin>
>> <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 : monu46010 at yahoo.com <mailto:monu46010 at 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<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 : monu46010 at yahoo.com
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