答复: [gmx-users] topology file of ligand

[sunyeping]

Thank you Dr. Lemkul,
 
Could you recommand some primary literatures which are most usefule for me to understand the force field? 

Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

------------------------------------------------------------------发件人：Justin Lemkul <jalemkul at vt.edu>发送时间：2013年10月16日(星期三) 00:05收件人：gromacs <gmx-users at gromacs.org>主　题：Re: [gmx-users] topology file of ligandOn 10/15/13 11:24 AM, sunyeping wrote:> Dear gromacs users,>> I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he immediately notice three things that are wrong with this topology, which include charge group, H atom charge, etc.> And the author then reconstructed a topology file. I don't understand how the charge group and charge of individual atom are correctly assigned. Could you explain it to me?>The Gromos96 parameter sets assign charges and charge groups based on chemical functional groups that are transferable between molecules. Spotting inaccuracies and knowing how to fix them come with understanding how the force field was derived (read the primary literature and study existing molecules).-Justin-- ==================================================Justin A. Lemkul, Ph.D.Postdoctoral FellowDepartment of Pharmaceutical SciencesSchool of PharmacyHealth Sciences Facility II, Room 601University of Maryland, Baltimore20 Penn St.Baltimore, MD 21201jalemkul at outerbanks.umaryland.edu | (410) 706-7441==================================================-- gmx-users mailing list gmx-users at gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-users* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists