Re: [gmx-users] how to get Eigenvectors

[Tsjerk Wassenaar]

Hi Nahren,

You can try the .g96 format for this, which has high precision. To
understand the format, convert something to .g96 and replace the
coordinates with the eigenvectors.

Hope it helps,

Tsjerk


On Fri, Nov 1, 2013 at 4:10 AM, nahren manuel meetnah...@yahoo.com wrote:

 Dear GMX Users,

 I performed an ANM calculation at
 http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi


 It returned me eigenvectors  in the following format (where the second and
 third column represent first and second eigenvector)

 1  0.010551 -0.048553
 1 -0.022038 -0.042918

 1  0.107906  0.045009

 2  0.007908 -0.061543

 2 -0.002990 -0.054203

 2  0.109087  0.062326

 .
 .
 I tried to convert them into trr file, so that I can use them for analysis
 and this is where I am stuck. I converted them to PDB and I loose out on
 the precision of coordinates.
 ATOM  1  CA  LYS A   1   0.011  -0.022   0.108  1.00 10.00
   C
 ATOM  2  CA  ILE A   2   0.008  -0.003   0.109  1.00 10.00
   C
 ATOM  3  CA  GLU A   3   0.008   0.011   0.077  1.00 10.00
   C

 I added the reference structure (the structure I submitted to the server
 as frame 1, time 0) to the above PDB file and used g_nmtraj to get the
 projection. Is there a better way to get the eigenvec.trr.

 The server also returns Hessian, so can I use this information to get the
 eigenvec.trr using g_nmeig, but I am not sure how the format of nm.mtx
 should be. Can someone advice me on how to proceed further.

 Sincerely,
 nahren
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-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
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[gmx-users] how to get Eigenvectors

[nahren manuel]

Dear GMX Users,

I performed an ANM calculation at 
http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi


It returned me eigenvectors  in the following format (where the second and 
third column represent first and second eigenvector)

1  0.010551 -0.048553
1 -0.022038 -0.042918 

1  0.107906  0.045009

2  0.007908 -0.061543

2 -0.002990 -0.054203 

2  0.109087  0.062326

.
.
I tried to convert them into trr file, so that I can use them for analysis and 
this is where I am stuck. I converted them to PDB and I loose out on the 
precision of coordinates.
ATOM      1  CA  LYS A   1       0.011  -0.022   0.108  1.00 10.00           C
ATOM      2  CA  ILE A   2       0.008  -0.003   0.109  1.00 10.00           C
ATOM      3  CA  GLU A   3       0.008   0.011   0.077  1.00 10.00           C

I added the reference structure (the structure I submitted to the server as 
frame 1, time 0) to the above PDB file and used g_nmtraj to get the projection. 
Is there a better way to get the eigenvec.trr.  

The server also returns Hessian, so can I use this information to get the 
eigenvec.trr using g_nmeig, but I am not sure how the format of nm.mtx should 
be. Can someone advice me on how to proceed further.

Sincerely,
nahren
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
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