Re: [gmx-users] make_ndx: duplicates groups appearing in index.ndx file

2012-07-31 Thread Justin Lemkul 



On 7/31/12 10:14 AM, Laura Kingsley wrote:

Hello,

I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm having an
issue with make_ndx. Using the old version I have a single group showing up for
each "odd" residue, eg JJJ shows up once as group 16 for example. When I use the
new version on the same file I get 2 groups appearing for residue JJJ and
others. Here is the output of that I get from make_ndx. Is there some way I can
prevent this?



Repeated groups are normal, but certainly undesirable. Since there is nothing 
functionally wrong with these groups, it's a rather low-priority bug and has 
been around since Gromacs 4.5 (so several years). The only way to prevent the 
duplicate groups would be to create an index file that eliminates the duplicates.


-Justin


  0 System  : 126928 atoms
   1 Other   :   137 atoms
   2 NGL : 9 atoms
   3 CY1 :10 atoms
   4 CAR :25 atoms
   5 HEM :73 atoms
   6 JJJ : 1 atoms
   7 CPZ :19 atoms
   8 Cl  : 6 atoms
   9 Protein :  7475 atoms
  10 Protein-H   :  3733 atoms
  11 C-alpha :   461 atoms
  12 Backbone:  1383 atoms
  13 MainChain   :  1844 atoms
  14 MainChain+Cb:  2275 atoms
  15 MainChain+H :  2275 atoms
  16 SideChain   :  5200 atoms
  17 SideChain-H :  1889 atoms
  18 Prot-Masses :  7475 atoms
  19 non-Protein : 119453 atoms
  20 Water   : 119310 atoms
  21 SOL : 119310 atoms
  22 non-Water   :  7618 atoms
  23 Ion : 6 atoms
  24 NGL : 9 atoms
  25 CY1 :10 atoms
  26 CAR :25 atoms
  27 HEM :73 atoms
  28 JJJ : 1 atoms
  29 CPZ :19 atoms
  30 Cl  : 6 atoms
  31 Water_and_ions  : 119316 atoms


Thanks,

- Laura



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] make_ndx: duplicates groups appearing in index.ndx file

2012-07-31 Thread Laura Kingsley 

Hello,

I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm 
having an issue with make_ndx. Using the old version I have a single 
group showing up for each "odd" residue, eg JJJ shows up once as group 
16 for example. When I use the new version on the same file I get 2 
groups appearing for residue JJJ and others. Here is the output of that 
I get from make_ndx. Is there some way I can prevent this?


 0 System  : 126928 atoms
  1 Other   :   137 atoms
  2 NGL : 9 atoms
  3 CY1 :10 atoms
  4 CAR :25 atoms
  5 HEM :73 atoms
  6 JJJ : 1 atoms
  7 CPZ :19 atoms
  8 Cl  : 6 atoms
  9 Protein :  7475 atoms
 10 Protein-H   :  3733 atoms
 11 C-alpha :   461 atoms
 12 Backbone:  1383 atoms
 13 MainChain   :  1844 atoms
 14 MainChain+Cb:  2275 atoms
 15 MainChain+H :  2275 atoms
 16 SideChain   :  5200 atoms
 17 SideChain-H :  1889 atoms
 18 Prot-Masses :  7475 atoms
 19 non-Protein : 119453 atoms
 20 Water   : 119310 atoms
 21 SOL : 119310 atoms
 22 non-Water   :  7618 atoms
 23 Ion : 6 atoms
 24 NGL : 9 atoms
 25 CY1 :10 atoms
 26 CAR :25 atoms
 27 HEM :73 atoms
 28 JJJ : 1 atoms
 29 CPZ :19 atoms
 30 Cl  : 6 atoms
 31 Water_and_ions  : 119316 atoms


Thanks,

- Laura

--
Laura Kingsley

Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643

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