ADL: covalent ligand with rigid receptor

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

ADL: covalent ligand with rigid receptor

gizem tatar
Hello;

I'm trying the covalent-tutorial protocol with example files.But this
tutorial don't give information about prepare the
3c9w_ligandwithsidechain_random.pdbqt file.How is this file prepared?

--




*Gizem Tatar, PhD candidateDepartment of Bioinformatics and Computational
Biology,*
*Institute of Health Sciences,Gaziantep University*
*Gaziantep TURKEY,+9027310*


*Phone : +90 342 317 1810 <%2B90%20342%20317%201810>Fax :     +90 342 360
1032 <%2B90%20342%20360%201032> *
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: covalent ligand with rigid receptor

Michel Sanner
To covalently  dock a ligand you need to graft some receptor atoms to it. The 2 atoms defining the covalent bond between atoms al from the ligand and atom ar from the ligand as well as a neighbor atom of ar must appear in both the ligand and the receptor structure. For instance, of you covalently attach to a cysteine using the SG-ligAt bond you need to attach the SG and  and CB atoms to ligAt. You can do this using the pylon builder for instance.

On Dec 3, 2017, at 7:59 AM, gizem tatar <[hidden email]<mailto:[hidden email]>> wrote:

Hello;

I'm trying the covalent-tutorial protocol with example files.But this
tutorial don't give information about prepare the
3c9w_ligandwithsidechain_random.pdbqt file.How is this file prepared?

--




*Gizem Tatar, PhD candidateDepartment of Bioinformatics and Computational
Biology,*
*Institute of Health Sciences,Gaziantep University*
*Gaziantep TURKEY,+9027310*


*Phone : +90 342 317 1810 <%2B90%20342%20317%201810>Fax :     +90 342 360
1032 <%2B90%20342%20360%201032> *
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---