Hi
remove Hydrogen atom of MET befor loading molecule to tleap because in amber
N-terminal residue have three hydrogen and your structure have single hydrogen
and there is no atom type for N-terminal residue having single hydrogen.
You remove this single hydrogen and load it tleap,hydrogen atom will be added
itself by tleap and will generate topology file.
> Hello,
> I have been trying generate topology file for the lux protein, 1y6D-H.pdb.
> The structure is a NMR structure taken from pdb, the first model is used
> and the reduce program has been employed to add H atoms. The leap input
> file is pasted below:
>
> source leaprc.ff99SB
> b= loadpdb 1y6D-H.pdb
> saveamberparm b 1y6D-only.top 1y6D-only.crd
> #savepdb b 1y6D-only-leap.pdb
> quit
>
> The topology file was not generated and the error message has been saved in
> the file 1y6d-leap-error, attached with the mail along with the input pdb
> structure. Any help would be useful.
>
> Thanks in advance,
> --
> Devlina Chakravarty
> JRF
> Bose Institute
> Kolkata
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>
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
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Received on Thu Jan 05 2012 - 07:00:03 PST
