Dear Amber
I am trying to upload the file in tleap,
i followed these step
tleap
source leaprc.ff99SB
Loading parameters: /usr/local/bio/amber12/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /usr/local/bio/amber12/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /usr/local/bio/amber12/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/bio/amber12/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/bio/amber12/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/bio/amber12/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/bio/amber12/dat/leap/lib/ions94.lib
Loading library: /usr/local/bio/amber12/dat/leap/lib/solvents.lib
libraries were loaded see the nucleic acid in red.
ligSeq = {ADE}
LIG = loadpdbUsingSeq ./temp.pdb ligSeq
loadPdbUsingSeq: ADE is not a unit!
Not loaded
here is the ADE pdb file
ATOM 1307 P A B 165 12.916 21.146 80.635 1.00906.37
P
ATOM 1308 OP1 A B 165 12.438 21.940 81.789 1.00906.37
O
ATOM 1309 OP2 A B 165 13.484 19.798 80.866 1.00906.37
O
ATOM 1310 O5' A B 165 11.910 21.186 79.378 1.00906.37
O
ATOM 1311 C5' A B 165 11.137 22.290 79.018 1.00906.37
C
ATOM 1312 C4' A B 165 11.807 22.786 77.705 1.00906.37
C
ATOM 1313 O4' A B 165 11.442 21.933 76.589 1.00906.37
O
ATOM 1314 C1' A B 165 10.599 22.537 75.683 1.00906.37
C
ATOM 1315 C5 A B 165 7.300 21.823 76.161 1.00906.37
C
ATOM 1316 N7 A B 165 7.388 21.069 75.543 1.00906.37
N
ATOM 1317 C8 A B 165 8.204 21.877 74.800 1.00906.37
C
ATOM 1318 N9 A B 165 9.133 22.093 75.810 1.00906.37
N
ATOM 1319 N1 A B 165 6.368 20.489 77.020 1.00906.37
N
ATOM 1320 C2 A B 165 7.551 20.089 77.869 1.00906.37
C
ATOM 1321 N3 A B 165 8.688 20.855 77.885 1.00906.37
N
ATOM 1322 C4 A B 165 8.375 21.772 76.918 1.00906.37
C
ATOM 1323 C6 A B 165 6.252 21.618 76.447 1.00906.37
C
ATOM 1324 N6 A B 165 5.367 22.495 76.549 1.00906.37
N
ATOM 1325 C2' A B 165 10.896 24.000 75.675 1.00906.37
C
ATOM 1326 O2' A B 165 9.741 24.730 75.321 1.00906.37
O
ATOM 1327 C3' A B 165 11.063 24.117 77.238 1.00906.37
C
ATOM 1328 O3' A B 165 9.779 24.130 77.973 1.00906.37
O
I also try this
ligSeq = {A}
LIG = loadpdbUsingSeq ./temp.pdb ligSeq
loadPdbUsingSeq: A is not a unit!
same error
Please guide if the file format of nucleotides is fine. How can I resolve
this issue. thanks
Best Wishes
Rehan
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Received on Thu Aug 05 2021 - 10:00:02 PDT
