Hi Pinke,

I work only in Linux OS, and the command for  this sort of conversion look like this:

$SCHRODINGER/utilities/structconvert -ipdb 1atp.pdb -omae merged.mae -a

The above mention commad have the -a option which is not supported when using the multiple PDB format. It is recommended and advice to use -a flag only with single pdb file. For this you need to convert all your PDB files separately and then combine them into one .mae file. 

Thanks

Thank you veryyy much for your reply, but im using windows :( thank u anyways :)

Hi Pinke,

I will suggest you to please install Cygwin https://www.cygwin.com/ and run the command line. You can find several schrodinger FAQ at http://www.schrodinger.com/kb/all/

Thanks

Thanks for ur reply, yes i use cygwin occasionally, please tell me how to proceed further and what command to run on it, iam from lifesciences stream new to bioinfo line, so please could you kindly explain it in detail.

thank u