Hi Rana,
Do you mean you meet the error for this command ”antechamber -fi pdb -fo mol2 -i 1DX_H_renum.pdb -o 1DX.mol2 -c bcc -pf y -nc”? First, note that you don’t have a number after the -nc option. Second, the error may be related to the protonation state of your ligand (e.g. making it has a odd number of electrons in your system).
Using reduce to add the hydrogen atoms by “reduce 1DX.pdb > 1DX_H.pdb” and then run the antechamber command :”antechamber -fi pdb -fo mol2 -i 1DX_H.pdb -o 1DX.mol2 -c bcc -pf y” can work. However, after checking the system by eyes, the charge of the ligand should be -2 after adding hydrogen atoms by reduce. So “antechamber -fi pdb -fo mol2 -i 1DX_H.pdb -o 1DX.mol2 -c bcc -pf y -nc -2” should be used under this situation.
However, there is also no grantee the protonation state determined by reduce is correct, and it is better to check by your own eyes through a visualization program (e.g. VMD) before performing the antechamber procedure.
Kind regards,
Pengfei
>
> On Sep 16, 2017, at 2:20 PM, Rana Rehan Khalid <rrkhalid.umich.edu> wrote:
>
> 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 Tue Sep 19 2017 - 20:30:02 PDT
