*ATOM 1 N LYS 1 3.993 88.616 32.608 1.00 0.00*
ATOM 2 H1 LYS 1 5.003 88.616 32.608 1.00 0.00
ATOM 3 H2 LYS 1 3.668 89.572 32.608 1.00 0.00
ATOM 4 H3 LYS 1 3.668 87.973 33.316 1.00 0.00
ATOM 5 CA LYS 1 3.543 88.059 31.348 1.00 0.00
ATOM 6 HA LYS 1 2.941 87.170 31.538 1.00 0.00
ATOM 7 CB LYS 1 2.696 89.064 30.575 1.00 0.00
ATOM 8 HB2 LYS 1 1.823 89.336 31.167 1.00 0.00
ATOM 9 HB3 LYS 1 3.288 89.956 30.370 1.00 0.00
ATOM 10 CG LYS 1 2.243 88.441 29.259 1.00 0.00
ATOM 11 HG2 LYS 1 3.116 88.169 28.666 1.00 0.00
ATOM 12 HG3 LYS 1 1.651 87.549 29.463 1.00 0.00
ATOM 13 CD LYS 1 1.396 89.446 28.485 1.00 0.00
ATOM 14 HD2 LYS 1 0.523 89.718 29.078 1.00 0.00
ATOM 15 HD3 LYS 1 1.988 90.338 28.280 1.00 0.00
ATOM 16 CE LYS 1 0.943 88.823 27.169 1.00 0.00
ATOM 17 HE2 LYS 1 1.816 88.551 26.576 1.00 0.00
ATOM 18 HE3 LYS 1 0.351 87.931 27.374 1.00 0.00
ATOM 19 NZ LYS 1 0.127 89.792 26.424 1.00 0.00
ATOM 20 HZ1 LYS 1 0.676 90.618 26.234 1.00 0.00
ATOM 21 HZ2 LYS 1 -0.173 89.379 25.552 1.00 0.00
ATOM 22 HZ3 LYS 1 -0.682 90.044 26.973 1.00 0.00
ATOM 23 C LYS 1 4.722 87.670 30.469 1.00 0.00
ATOM 24 O LYS 1 5.875 87.842 30.859 1.00 0.00
*TER *
ATOM 25 HH31 ACE 2 6.214 89.036 33.366 1.00 0.00
ATOM 26 CH3 ACE 2 5.822 88.019 33.366 1.00 0.00
ATOM 27 HH32 ACE 2 6.170 87.495 34.256 1.00 0.00
ATOM 28 HH33 ACE 2 6.170 87.495 32.476 1.00 0.00
ATOM 29 C ACE 2 4.292 88.019 33.366 1.00 0.00
ATOM 30 O ACE 2 3.668 89.078 33.366 1.00 0.00
*ATOM 31 N LYS 3 3.986 88.587 32.553 1.00 0.00*
ATOM 32 H LYS 3 4.139 88.064 33.403 1.00 0.00
ATOM 33 CA LYS 3 4.890 88.368 31.441 1.00 0.00
ATOM 34 HA LYS 3 4.307 88.022 30.587 1.00 0.00
ATOM 35 CB LYS 3 5.609 89.666 31.050 1.00 0.00
ATOM 36 HB2 LYS 3 4.837 90.406 30.838 1.00 0.00
ATOM 37 HB3 LYS 3 6.187 89.983 31.918 1.00 0.00
ATOM 38 CG LYS 3 6.532 89.537 29.845 1.00 0.00
ATOM 39 HG2 LYS 3 6.997 90.505 29.661 1.00 0.00
ATOM 40 HG3 LYS 3 7.303 88.802 30.077 1.00 0.00
ATOM 41 CD LYS 3 5.768 89.096 28.602 1.00 0.00
ATOM 42 HD2 LYS 3 6.480 88.971 27.786 1.00 0.00
ATOM 43 HD3 LYS 3 5.288 88.140 28.814 1.00 0.00
ATOM 44 CE LYS 3 4.709 90.118 28.200 1.00 0.00
ATOM 45 HE2 LYS 3 4.044 90.264 29.052 1.00 0.00
ATOM 46 HE3 LYS 3 5.217 91.055 27.971 1.00 0.00
ATOM 47 NZ LYS 3 3.908 89.681 27.011 1.00 0.00
ATOM 48 HZ1 LYS 3 3.437 88.813 27.223 1.00 0.00
ATOM 49 HZ2 LYS 3 3.224 90.390 26.787 1.00 0.00
ATOM 50 HZ3 LYS 3 4.524 89.546 26.222 1.00 0.00
Are you trying to extract the 3rd reisude and just cap that one residue?
Currently you have *two lysines on top of each other. *If you are trying to
just extract the lysine, you can Take ACE2-LYS3-SER4 and put that in a
separate text file. Change SER to NME.
Keep only the first 3 lines:
ATOM 55 N *NME* 4 6.394 86.595 30.724 1.00 0.00
ATOM 56 H *NME* 4 6.044 86.786 29.796 1.00 0.00
ATOM 57 CA *NME* 4 7.372 85.526 30.887 1.00 0.00
LEAP will add the remaining atoms.
Also, your TER marker in there between residues 1 and 2 is being treated as
a chain termination. Remove the TER card.
On Fri, Jun 16, 2017 at 12:04 AM, Saikat Pal <saikatpaliitg.yahoo.com>
wrote:
> After capping of ACE (according to the manual) I have got 2rd6-leap-1.pdb
> where one H of ACE are merged with the another C of the LYS and also there
> is no bond between C (with O) of the Carbonyl of ACE and N of LYS.I have
> tried other Protein PDB but there is the same problem. What is the
> procedure to capping with ACE of an N-terminal protein ??
>
>
> On Friday, 16 June 2017 1:04 AM, David Case <david.case.rutgers.edu>
> wrote:
>
>
> On Thu, Jun 15, 2017, Saikat Pal wrote:
>
> > Thank you, sir, for your reply .
>
> As far as I can tell(?), your second email is just a copy of the original
> email. You don't make it clear that you tried the suggestions I gave, or
> made
> any attempt to answer the questions I posed.
>
> ....dac
>
>
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--
Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
Luo Lab, http://rayl0.bio.uci.edu/html/
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)
aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
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Received on Wed Jun 21 2017 - 10:00:03 PDT
