From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jun 15 2006 - 14:48:48 CDT
Dear Morad,
the oxygens are there; they are just in a different part of the residue.
Please look at atoms 388-390.
Best,
Peter
Morad Alawneh wrote:
> Thanks.
>
> using none option:
> segment M2A {
> first none
> last none
> auto none
> pdb ChainB.pdb
> }
> gives the following (part of my pdb):
>
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 1 N SER M 1 11.840 11.049 -13.315 1.00
> 0.00 M2A N
> ATOM 2 HN SER M 1 11.839 10.069 -13.117 0.00
> 0.00 M2A H
> ATOM 3 CA SER M 1 10.683 11.367 -14.235 1.00
> 0.00 M2A C
> ATOM 4 HA SER M 1 10.554 12.439 -14.168 0.00
> 0.00 M2A H
> ATOM 5 CB SER M 1 11.056 10.956 -15.697 1.00
> 0.00 M2A C
> ATOM 6 HB1 SER M 1 11.559 9.963 -15.660 0.00
> 0.00 M2A H
> ATOM 7 HB2 SER M 1 10.136 10.834 -16.312 0.00
> 0.00 M2A H
> ATOM 8 OG SER M 1 11.950 11.906 -16.281 1.00
> 0.00 M2A O
> ATOM 9 HG1 SER M 1 12.317 11.499 -17.076 0.00
> 0.00 M2A H
> ATOM 10 C SER M 1 9.372 10.723 -13.793 1.00
> 0.00 M2A C
> ATOM 11 O SER M 1 9.276 10.072 -12.756 1.00
> 0.00 M2A O
>
> ATOM 386 N LEU M 25 3.874 -12.200 11.837 1.00
> 0.00 M2A N
> ATOM 387 HN LEU M 25 4.328 -11.710 11.095 0.00
> 0.00 M2A H
> ATOM 388 CA LEU M 25 4.247 -13.595 11.944 1.00
> 0.00 M2A C
> ATOM 389 HA LEU M 25 3.322 -14.147 12.047 0.00
> 0.00 M2A H
> ATOM 390 CB LEU M 25 5.044 -13.983 10.669 1.00
> 0.00 M2A C
> ATOM 391 HB1 LEU M 25 4.430 -13.675 9.791 0.00
> 0.00 M2A H
> ATOM 392 HB2 LEU M 25 5.973 -13.373 10.624 0.00
> 0.00 M2A H
> ATOM 393 CG LEU M 25 5.396 -15.479 10.503 1.00
> 0.00 M2A C
> ATOM 394 HG LEU M 25 5.991 -15.763 11.404 0.00
> 0.00 M2A H
> ATOM 395 CD1 LEU M 25 4.148 -16.375 10.386 1.00
> 0.00 M2A C
> ATOM 396 HD11 LEU M 25 4.442 -17.434 10.220 0.00
> 0.00 M2A H
> ATOM 397 HD12 LEU M 25 3.540 -16.323 11.315 0.00
> 0.00 M2A H
> ATOM 398 HD13 LEU M 25 3.513 -16.054 9.533 0.00
> 0.00 M2A H
> ATOM 399 CD2 LEU M 25 6.285 -15.673 9.267 1.00
> 0.00 M2A C
> ATOM 400 HD21 LEU M 25 6.558 -16.744 9.152 0.00
> 0.00 M2A H
> ATOM 401 HD22 LEU M 25 5.770 -15.355 8.338 0.00
> 0.00 M2A H
> ATOM 402 HD23 LEU M 25 7.223 -15.085 9.366 0.00
> 0.00 M2A H
> ATOM 403 C LEU M 25 5.090 -13.876 13.180 1.00
> 0.00 M2A C
> ATOM 404 O LEU M 25 4.887 -14.871 13.881 1.00
> 0.00 M2A O
>
>
>
>
> using NTER and CTER option:
> segment M2A {
> first NTER
> last CTER
> auto none
> pdb ChainB.pdb
> }
> gives the following (part of my pdb):
>
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 1 N SER M 1 11.829 11.066 -13.332 1.00
> 0.00 M2A N
> ATOM 2 HT1 SER M 1 12.653 11.516 -13.677 0.00
> 0.00 M2A H
> ATOM 3 HT2 SER M 1 11.965 10.076 -13.311 0.00
> 0.00 M2A H
> ATOM 4 HT3 SER M 1 11.617 11.401 -12.414 0.00
> 0.00 M2A H
> ATOM 5 CA SER M 1 10.672 11.384 -14.252 1.00
> 0.00 M2A C
> ATOM 6 HA SER M 1 10.543 12.456 -14.185 0.00
> 0.00 M2A H
> ATOM 7 CB SER M 1 11.045 10.973 -15.714 1.00
> 0.00 M2A C
> ATOM 8 HB1 SER M 1 11.548 9.980 -15.677 0.00
> 0.00 M2A H
> ATOM 9 HB2 SER M 1 10.125 10.851 -16.329 0.00
> 0.00 M2A H
> ATOM 10 OG SER M 1 11.939 11.923 -16.298 1.00
> 0.00 M2A O
> ATOM 11 HG1 SER M 1 12.306 11.516 -17.093 0.00
> 0.00 M2A H
> ATOM 12 C SER M 1 9.361 10.740 -13.810 1.00
> 0.00 M2A C
> ATOM 13 O SER M 1 9.265 10.089 -12.773 1.00
> 0.00 M2A O
>
> ATOM 388 C LEU M 25 5.079 -13.859 13.163 1.00
> 0.00 M2A C
> ATOM 389 OT1 LEU M 25 5.211 -13.006 13.668 0.00
> 0.00 M2A O
> ATOM 390 OT2 LEU M 25 5.307 -14.832 13.187 0.00
> 0.00 M2A O
> ATOM 391 N LEU M 25 3.863 -12.183 11.820 1.00
> 0.00 M2A N
> ATOM 392 HN LEU M 25 4.317 -11.693 11.078 0.00
> 0.00 M2A H
> ATOM 393 CA LEU M 25 4.236 -13.578 11.927 1.00
> 0.00 M2A C
> ATOM 394 HA LEU M 25 3.311 -14.130 12.030 0.00
> 0.00 M2A H
> ATOM 395 CB LEU M 25 5.033 -13.966 10.652 1.00
> 0.00 M2A C
> ATOM 396 HB1 LEU M 25 4.419 -13.658 9.774 0.00
> 0.00 M2A H
> ATOM 397 HB2 LEU M 25 5.962 -13.356 10.607 0.00
> 0.00 M2A H
> ATOM 398 CG LEU M 25 5.385 -15.462 10.486 1.00
> 0.00 M2A C
> ATOM 399 HG LEU M 25 5.980 -15.746 11.387 0.00
> 0.00 M2A H
> ATOM 400 CD1 LEU M 25 4.137 -16.358 10.369 1.00
> 0.00 M2A C
> ATOM 401 HD11 LEU M 25 4.431 -17.417 10.203 0.00
> 0.00 M2A H
> ATOM 402 HD12 LEU M 25 3.529 -16.306 11.298 0.00
> 0.00 M2A H
> ATOM 403 HD13 LEU M 25 3.502 -16.037 9.516 0.00
> 0.00 M2A H
> ATOM 404 CD2 LEU M 25 6.274 -15.656 9.250 1.00
> 0.00 M2A C
> ATOM 405 HD21 LEU M 25 6.547 -16.727 9.135 0.00
> 0.00 M2A H
> ATOM 406 HD22 LEU M 25 5.759 -15.338 8.321 0.00
> 0.00 M2A H
> ATOM 407 HD23 LEU M 25 7.212 -15.068 9.349 0.00
> 0.00 M2A H
>
>
>
>
> /*Morad Alawneh*/
>
> *Department of Chemistry and Biochemistry*
>
> *C100 BNSN, BYU*
>
> *Provo, UT 84602*
>
>
>
> Peter Freddolino wrote:
>> Dear Morad,
>> could you please be more specific as to what did happen? Giving
>> excerpts from your pdb before and after running psfgen would be
>> helpful, so we can see if any changes did occur, and what your atom
>> naming looks like.
>>
>> Best,
>> Peter
>>
>> Morad Alawneh wrote:
>>> Dear users,
>>>
>>>
>>> When I tried to build a segment using vmd, the option "last CTER"
>>> did not do what it show do, i.e: replace C=O by O-C=O. This is how I
>>> did it
>>>
>>> segment M2A {
>>> first NTER
>>> last CTER
>>> auto none
>>> pdb ChainA.pdb
>>> }
>>>
>>>
>>> Any idea about this problem?
>>>
>>> Thanks
>>>
>>> --
>>>
>>>
>>>
>>> /*Morad Alawneh*/
>>>
>>> *Department of Chemistry and Biochemistry*
>>>
>>> *C100 BNSN, BYU*
>>>
>>> *Provo, UT 84602*
>>>
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