Aligning ligand based pharmacophore to a protein cavity based pharmacophore

[ja...@vclinbio.com]

Dear Silicos Admin,

Firstly, thank you for providing the software 'Align-it' freely for academic use.

Iam trying to align a ligand based pharmacophore to a protein cavity based pharmacophore. Iam having difficulty with it.

1) The protein cavity based pharmacophore was generated by 'ligbuilder'

2) I took the output of 'ligbuilder's' protein based pharmacophore in pdb format and generated a phar file using 'align-it'

align-it -d Prot.pdb -p Prot.phar -m

3) I also generated a PHAR file for a ligand

align-it -d Lig.pdb -p Lig.phar -m

4) When i tried to align lig.phar using Prot.phar as reference, i got unexplainable results.

align-it --reference Prot.phar --refType PHAR -d Lig.phar --dbType PHAR --p output_prot.phar --scores result_prot.tab

contents of result_prot.tab:
    nan        258.113    nan    0    nan    3    0    0    0

5) When also tried to align Prot.phar against Prot.phar itself as a reference, still iam getting unexplainable results.

align-it --reference Prot.phar --refType PHAR -d Prot.phar --dbType PHAR --p output_prot_self.phar --scores result_prot_self.tab

contents of result_prot_self.tab
    nan        nan    nan    0    nan    9    0    0    0


I have attached all the input files for your kind perusal.

Can you kindly advice  me how to go about.

Thank you,
Jana.K