AMBER Archive (2009)

Subject: [AMBER] RE:xleap problem

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Mon Jan 26 2009 - 13:48:11 CST

Dear D Case,

I again run some experiments according to your advices and my min.out file is like in below. I used packmol,  I wrote box size for x, y, z : 9.825 A and created a packmol pdb file for this system. So I didn't use solvatebox command in xleap. I thought that there is a problem about using packmol. If so, How can I solve this problem  and use packmol without any errors ? In this sense, I'm waiting for your help and also other people's help  who have enough experience on PACKMOL package. Or I'm waiting for some alternative solutions of you related with LEAP.

Sincerely,

 -------------------------------------------------------
          Amber 10 SANDER                              2008
          -------------------------------------------------------

| PMEMD implementation of SANDER, Release 10

| Run on 01/26/2009 at 15:55:22

  [-O]verwriting output

File Assignments:
|   MDIN: /home_palamut2/ogurbulak/c7AMBER10/min/min.in                        
|  MDOUT: /home_palamut2/ogurbulak/c7AMBER10/min/min.out                       
| INPCRD: /home_palamut2/ogurbulak/c7AMBER10/n-dodecane.inpcrd                 
|   PARM: /home_palamut2/ogurbulak/c7AMBER10/n-dodecane.prmtop                 
| RESTRT: /home_palamut2/ogurbulak/c7AMBER10/min/n-dodecane.rst                
|   REFC: refc                                                                 
|  MDVEL: mdvel                                                                
|   MDEN: mden                                                                 
|  MDCRD: mdcrd                                                                
| MDINFO: mdinfo                                                               
|LOGFILE: logfile                                                              

 
 Here is the input file:
 
initial minimization                                                          
 &cntrl                                                                       
  imin=1,                                                                     
  maxcyc=500,                                                                 
  ncyc=250,                                                                   
  ntb=1,                                                                      
  cut=9.825,                                                                  
  ntpr=100,                                                                   
  ntc=2, ntf=2,                                                               
 /                                                                            
                                                                              
| ERROR:   Box parameters not found in inpcrd file!


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