[AMBER] The problem for image tool in AMBER

From: ³ <lujb15.mails.tsinghua.edu.cn>
Date: Thu, 4 May 2017 11:20:58 +0800 (GMT+08:00)

Dear all:
   I have done a molecular dynamics. But I encounter a problem when I see the structure. The attached file am_cro_md.rst is my last structure of molecular dynamics trajectory, and md.in and am_cro.prmtop are the control and top files. I convert the structure to the pdb file using cpptraj:
   trajin am_cro_md.rst
   trajout am_cro_md1.pdb
   This structure seems no periodic. So I use the image tool:
   trajin am_cro_md.rst
   image center
   trajout am_cro_md2.pdb
   This two structures are different. The metal ion coordinates with two NO3- for first structure, but with three NO3- for second structure.They are so strange. I want to choose some solvent to do QM/MM optimization. So I do not know choose which structure. Is there something wrong? Can anyone give me a help?
   With my best regards,
   Junbo
    










_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 03 2017 - 20:30:02 PDT
Custom Search