Hi there,
I have this example:
Wsk.mol2 is the original input in mol2 format contains:
.<TRIPOS>ATOM
1 BR1 -0.2000 4.5430 1.6950 Br 1 WSK 0.0000
****
2 BR2 -7.5890 8.0800 4.4860 Br 1 WSK 0.0000
****
Applying command (from AT 1.3):
antechamber -fi mol2 -i Wsk.mol2 -fo mol2 -o WskAC.mol2
or
antechamber -fi mol2 -i Wsk.mol2 -fo pdb -o WskAC.pdb
I got in WskAC.mol2 (or could be PDB, whatever):
.<TRIPOS>ATOM
1 Br1 -0.2000 4.5430 1.6950 br 1 WSK 0.000000
2 Br2 -7.5890 8.0800 4.4860 br 1 WSK 0.000000
or
ATOM 1 Br1 WSK 1 -0.200 4.543 1.695
ATOM 2 Br2 WSK 1 -7.589 8.080 4.486
Did you notice the diff in BR1 to Br1? It sounds nothing but I am afraid it
has implications.
To name one and very important, according to PDB standard an atom name has
always to be upper case.
To name another problem, when using this pdb with CNS or Xplor-nih, they
will not recognise atom 'Br'.
It may be OK for Amber but since I see your efforts to make AMBER compliance
with PDB standards I thought I should call the attention here.
Best regards,
Alan
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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Received on Thu Mar 18 2010 - 10:30:04 PDT
