[gmx-users] RE : essential dynamics

[bharat gupta]

Hi,

After searching though gmxuserlist I found the relevant thread for ED... I
followed the following steps :-
1) g_covar - to generate a covariance matrix and diagonalize it (for c-alpha
atoms only)
2) g_anaeig - to generate eigen vectors
3)g_rmsf - for calculating RMSD of first 8 eigen vectors , I got an error at
this step that -

Fatal error:
Molecule in topology has atom numbers below and above natoms (230).
You are probably trying to use a trajectory which does not match the first
230 a
toms of the run input file.
You can make a matching run input file with tpbconv.
-------------------------------------------------------

"California, R.I.P." (Red Hot Chili Peppars)

4) then I used make_ndx - for generating an index file containing only
c-alpha atoms..which was done successfully
5) Further I used tpbconv - to generate a .tpr file for calculating the rmsf
... but I am getting the following error at this step ..

Fatal error:
Molecule in topology has atom numbers below and above natoms (230).
You are probably trying to use a trajectory which does not match the first
230 a
toms of the run input file.
You can make a matching run input file with tpbconv.
-------------------------------------------------------

"California, R.I.P." (Red Hot Chili Peppars)


Pls help what has to be done in order to generate the .tpr file ...


-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110131/c0b83da1/attachment.html>