AMBER Archive (2005)

Subject: Re: RE: Re: AMBER:

From: Zhiguo Liu (zgleo_at_tom.com)
Date: Sun Jul 10 2005 - 02:37:36 CDT

Dear glc0358,
     Full minimization is necessary for the stability of the system. Maybe you need to find out when the topology began to mess out. One way is to convert the trajectory to pdb format and check it in Rasmol or anything others. If all topologis in pdb are OK, that wouldn't be the problem of the trajectory. Maybe as Jufang said, you'd better try both "crd" and "crdbox" while loading trajectory. If simulation is in solvent and your trajectory is raw, "crdbox" is the right choice.

                
          
                                                             Zhiguo Liu
                                                        
                                                                  2005-7-10

___________________________________________
    
Zhiguo Liu
Ph.D candidate
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
Chinese Academy of Science
Shanghai, China
zhiguo.leo_at_gmail.com
___________________________________________

----- 2005-07-09, 18:37:54, glc0358 wrote -----
  RE: Re: AMBER:

>Dear Zhiguo Liu:
> Thank you for your help! Actually I visualized the trajectory by the prmtop file which I used for the minimization and MD. Maybe I should run the minimization for more time?
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