Re[2]: 回复： [gmx-users] No such moleculetype Na

[Иимяа Фаамиилиияа]

Change name Cl to name CL and check name Na in forcefield you use (it could be NA).


11 декабря 2011, 17:30 от Mark Abraham <Mark.Abraham at anu.edu.au>:
 
  
  
 
 On 11/12/2011 11:43 PM, yp sun wrote:    
 The name of ion is different when using different force field You can check which field force you use and find out how Na and Cl ion is written in this force field.
      
 The molecule name is constant over all force fields in the 4.5 series of GROMACS, and the molecule name is all that genion cares about. Atom and residue names might vary.
 
 Mark
 
    
 
 Yeping Sun
 CAS Key Laboratory of Pathogenic Microbiology & Immunology
 INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
 NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
 
 --- 11年12月11日，周日, Setare Jiji <jj.64fhony at yahoo.com> 写道：
 
 发件人: Setare Jiji <jj.64fhony at yahoo.com>
 主题: [gmx-users] No such moleculetype Na
 收件人: gmx-users at gromacs.org
 日期: 2011年12月11日,周日,下午5:17
 
 
   
  
   
 Hi,
 Thanks for your responding.
 
 I checked my ions.itp file in which file sodium and chlorine ions are as Na and Cl form.
 
 Thus, I used genion as follows:
 
 genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -nname Cl -nn 8 -pname Na
 
 Unfortunately, I encountered same fatal error.
 
 any help will highly appreciated.
 
           
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