Hi Hari If I understood you correctly, you want to modify and subsequently dock it onto a complex structure, right? For me, the following workflow turned out to be most straightfwd:
- build it in MOLOC (http://www.moloc.ch/). It lets you very easily modify an existing molecule without the need of a restraint file, or build a ligand from scratch. Adding atoms, change their H-counts, chirality, or adding bonds between two atoms is rather fast. Minimize the molecule either in vacuum or dock it right there on its substrate. If you need coot later on, store a pdb file and - create the restraints file via prodrg server (http://prodrg1.dyndns.org/submit.html). Its up to you to disable EM at this point to retain the conformation of your molecule - pre-load the cif file in coot and then load the pdb file that comes along with the prodrg run (prodrg might change atom names, so work with its outputs from now on) If you need help in moloc, send me a message. Its not a WYSIWYG layout but has some big advantages over coot in terms of picking and moving single chains, fragments or group of atoms. cheers, Matthias Dr. Matthias Barone AG Kuehne, Rational Drug Design Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany Phone: +49 (0)30 94793-284 ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Hari shankar <0000465d10db143e-dmarc-requ...@jiscmail.ac.uk> Sent: Saturday, June 13, 2020 6:50:51 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ligand building Hi all, I want to build a ligand that does not exist in reality (or be able to modify an existing ligand as per choice). 1. JLigand in the ccp4 suite seems to work only on java and gives me an “configuration problem” as an error message on my Windows. I am new to this and unaware of how to solve this issue. Could I get some suggestions on how to start this? 2. Alternatively, I was trying to use eLBOW from phenix but it seems to only build ligands but unable to delete atoms. Is there another program or option for me to delete sections of the ligand and geometrical optimise them in phenix? Thanks Hari ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
