H++ problem solved kindly guide only about
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.
On Sat, Sep 16, 2017 at 1:43 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> 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 - 12:30:04 PDT
