My system consist of bay60 compound as ligand. I am trying to produce its
frcmod and prep file by using mcpb.py module in amber. Can i handle this
compound through mcpb.py module because when I upload my system model on
H++ its shows error and for mol 2 generation
antechamber -fi pdb -fo mol2 -i 1DX_H_renum.pdb -o 1DX.mol2 -c bcc -pf y -nc
this command i used to generate mol2 for bay60(1DX) I used.
H++
FAILURE:
TECHNICAL DESCRIPTION: An error occured in the setup ( tleap ) step of
processing 0.15_80_10_pH6.5_H_4IAE. The auxillary program pdb2pqr.sh was
unable to produce the (AMBER format) files tmp.top and tmp.crd needed for
the next step.
PROBABLE CAUSE (1) The input 0.15_80_10_pH6.5_H_4IAE file contains very
nonstandard atom/residue names that were unrecognized.
PROBABLE CAUSE (2) The input 0.15_80_10_pH6.5_H_4IAE file has multiple
chains not separated by a TER.
PROBABLE CAUSE (3) The input 0.15_80_10_pH6.5_H_4IAE file contains DNA or
RNA with a 5' phosphate group.
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Received on Sat Sep 16 2017 - 11:00:03 PDT
