preparing receptor with coenzyme

[SoodabehGhaffari]

Hello, The receptor that I am using has a coenzyme (NADPH) which I would like to keep it during docking. If I do not keep it, the small molecule might clash with it. When I prepare the receptor with the command below, it will delete the coenzyme residue even though I added the flag not to do that. I really appreciate your help.

Thank you

[sg6615@della-gpu binding]$ prepare_receptor -r mytarget.pdb -A 'checkhydrogens' -U 'nphs_lps_waters' -e 'False'

Unable to assign HAD type to atom N Unable to assign valence to atom mytarget:A:ALA2:N type = N Unable to assign HAD type to atom N Unable to assign valence to atom mytarget:A:LEU5:N type = N Unable to assign HAD type to atom N Unable to assign valence to atom mytarget:A:ALA6:N type = N Sorry, there are no Gasteiger parameters available for atom mytarget:A:MET1:O Unable to assign MAP type to atom N Sorry, there are no Gasteiger parameters available for atom mytarget:A:ALA2:N Sorry, there are no Gasteiger parameters available for atom mytarget:A:ALA2:O Sorry, there are no Gasteiger parameters available for atom mytarget:A:ARG3:O Sorry, there are no Gasteiger parameters available for atom mytarget:A:PRO4:O Unable to assign MAP type to atom N Sorry, there are no Gasteiger parameters available for atom mytarget:A:LEU5:N Sorry, there are no Gasteiger parameters available for atom mytarget:A:LEU5:O Unable to assign MAP type to atom N Sorry, there are no Gasteiger parameters available for atom mytarget:A:ALA6:N 'Deleting non-standard residues:ANAP0 from mytarget_

[mamapapamoi22709004]

hi i have the same problem, did you solve it?

[rwxayheee]

Hi @mamapapamoi22709004 Can you share your input file? It should be possible to keep cofactors like NADPH because prepare_receptor does not delete non-protein groups if the chain isn't entirely made of nonstandard residues.