Incorrect handling of phenylalanine amide by antechamber 1.2 in amber
10 (or mishandling of antechamber by the operator).
Phenylalanine amide triprotonated at N, thus charge +1. The structure
is correct in both Chimera and VMD.
$AMBERHOME/exe/antechamber -i pha.NH3.pdb -fi pdb -o pha.prepin -fo
prepi -c bcc -s 2 -nc +1
$AMBERHOME/exe/parmchk -i pha.prepin -f prepi -o pha.frcmod
These prepin and frcmod file are not accepted by Chimera, while VMD
shows a highly deformed structure (much too long C=O bond, phenyl
hydrogens out of plane and ring distorted; NH3 also distorted.
Thanks for indicating my mistakes in the antechamber input files.
francesco pietra
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Received on Thu Sep 30 2010 - 02:30:03 PDT
