Hi AMBER people!
When saving a PDB file from leap my atom names are messed up. Below I have
pasted the output of the desc commant within tleap and the same atoms
grepped out of the PDB file when saved with savepdb. I had loaded
leaprc.ff99 and leaprc.gaff (using AMBER 8) and there is no addPdbAtomMap
entry for H[B,D,G][2,3]. Is this a bug or is this meant to be like this?
Thanks for any help!
Regards,
Hannes Barsch
> desc pep.2
RESIDUE name: PRO
RESIDUE sequence number: 2
RESIDUE PDB sequence number: 2
Type: protein
Connection atoms:
Connect atom 0: A<N 1>
Connect atom 1: A<C 13>
Improper torsions:
Contents:
A<O 14>
A<C 13>
A<HA 12>
A<CA 11>
A<HB3 10>
A<HB2 9>
A<CB 8>
A<HG3 7>
A<HG2 6>
A<CG 5>
A<HD3 4>
A<HD2 3>
A<CD 2>
A<N 1>
[hbarsch.barsch Leap]$ grep 'PRO 2' leap.pdb
ATOM 51 N PRO 2 4.908 -1.464 -2.158 1.00 0.00
ATOM 52 CD PRO 2 5.837 -1.132 -3.232 1.00 0.00
ATOM 53 2HD PRO 2 6.386 -0.227 -2.971 1.00 0.00
ATOM 54 3HD PRO 2 5.282 -0.966 -4.155 1.00 0.00
ATOM 55 CG PRO 2 6.722 -2.341 -3.306 1.00 0.00
ATOM 56 2HG PRO 2 7.745 -2.020 -3.502 1.00 0.00
ATOM 57 3HG PRO 2 6.388 -2.998 -4.109 1.00 0.00
ATOM 58 CB PRO 2 6.605 -3.025 -1.965 1.00 0.00
ATOM 59 2HB PRO 2 7.496 -2.814 -1.375 1.00 0.00
ATOM 60 3HB PRO 2 6.517 -4.101 -2.118 1.00 0.00
ATOM 61 CA PRO 2 5.344 -2.490 -1.229 1.00 0.00
ATOM 62 HA PRO 2 4.670 -3.346 -1.235 1.00 0.00
ATOM 63 C PRO 2 5.448 -1.937 0.186 1.00 0.00
ATOM 64 O PRO 2 5.118 -0.779 0.428 1.00 0.00
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Received on Fri May 20 2005 - 10:52:59 PDT
