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 <jalem...@vt.edu>发送时间:2013年10月16日(星期三) 00:05收件人:gromacs 
<gmx-users@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 21201jalem...@outerbanks.umaryland.edu | 
(410) 706-7441==================================================-- gmx-users 
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