You can make molecule in chemdraw or chemdraw 3d with proper bond order and save it in sdf or .mol format or any other format compatible with schrodinger. Schrodinger should be able to read .sdf or .mol format.
Dhiraj ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Nigel Moriarty <[email protected]> Sent: Thursday, July 7, 2022 7:30 PM To: [email protected] <[email protected]> Subject: [External] Re: [ccp4bb] Missing double bonds in the ligand Joel You'll need to be more specific than ".cif" files. CIF can be used for models, data and restraints. Read more here. http://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2013_01.pdf#page=6 If you are referring to the restraints CIF, it is possible but I'm not sure which software uses it. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov> ORCID : orcid.org/0000-0001-8857-9464<https://orcid.org/0000-0001-8857-9464> On Thu, Jul 7, 2022 at 3:06 PM Joel Tyndall <[email protected]<mailto:[email protected]>> wrote: Does the Schrodinger software read a .cif file? The bond order should be embedded in there. From: CCP4 bulletin board <[email protected]<mailto:[email protected]>> On Behalf Of Nigel Moriarty Sent: Friday, 8 July 2022 7:47 am To: [email protected]<mailto:[email protected]> Subject: Re: [ccp4bb] Missing double bonds in the ligand Further reading https://en.wikipedia.org/wiki/The_Treachery_of_Images<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FThe_Treachery_of_Images&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=W1W38k1ojjAqhp3ZjM81dMP86UMlp8bnnOYLg%2Bnk5AU%3D&reserved=0> https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2016_01.pdf#page=10<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fphenix-online.org%2Fphenixwebsite_static%2Fmainsite%2Ffiles%2Fnewsletter%2FCCN_2016_01.pdf%23page%3D10&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MuwAXaUsqCI4G6yAyVJimLn3I2JoX7JcFWlx4zIGFIE%3D&reserved=0> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected]<mailto:[email protected]> Fax : 510-486-5909 Web : CCI.LBL.gov<https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcci.lbl.gov%2F&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qFlMWmLOXzftylRuD%2BaySZgplAegttraaWnZA9Uaccw%3D&reserved=0> ORCID : orcid.org/0000-0001-8857-9464<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F0000-0001-8857-9464&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VXj9S5lltBHJubLfsQrPhvfTz8eOdhXwhOrtn7oCLHw%3D&reserved=0> On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten <[email protected]<mailto:[email protected]>> wrote: Dear Anil, Bond orders are not captured in PDB files explicitly. The way bonds are shown depends on the program and possibly additional information sources (i.e. molecular restraint or topology files). So this is just a "problem" with Schrödinger. Cheers, Robbie On 7 Jul 2022 21:00, "Dr. Anil Kumar Marapaka" <[email protected]<mailto:[email protected]>> wrote: Dear CCP4 Users, We are working on a ligand-bound structure and would like to look at protein-ligand interactions using Schrodinger. Molecule structure is: When we load the ligand-fitted PDB file into Schrodinger, the molecule appears to be flat like it should be in the structure but it removed all the double bonds in the ligand where the above shown original molecular structure has double bonds in it. When we load the same PDB file into pymol and look at the ligand it shows correctly We would appreciate if any insight or suggestions for why this may be happening and how to ensure the ligand shows properly when the PDB is loaded into Schrodinger. Would this be an issue with Schrodinger software or with the PDB file? I can be available by direct email for troubleshooting at [email protected]<mailto:[email protected]>. -- Anil Kumar Marapaka, Ph.D. Post-Doctoral Research Associate Department of Medicinal Chemistry and Molecular Pharmacology (MCMP), Purdue University, West lafayette, Indiana-47907, USA. 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