$a1 gets the file path,like C:Projecct\jeisika\mol.pdb
which i plan to open and analyze, whereas, when made to run on server this file path comes to perl file as "mol.pdb" only!

Why do you need the entire path to the file?  On the remote machine you have a different file system, where that path will most likely not be valid anyway...  Most browsers (except some versions of IE) are aware of this, and simply strip the directory component of the local path — in part because it may unnecessarily disclose private details of your local machine.

If you want to analyse the contents of the file, there is no way around uploading those contents to the server, as the server cannot access C:Projecct\jeisika\mol.pdb on your local filesystem.  Read what the Anonymous Monk pointed to on how to upload files via CGI.

In reply to Re^3: Upload file (PDB format ) on server by almut
in thread Upload file (PDB format ) on server by flyPerl

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