[gmx-users] RMSD average structure

[Andrea Carotti]

Hi,
    I have a long md run of 1800 frames and I' ve seen that it's ok.
Now I'm trying to analyze it with g_rmsf to obtain an average structure with the b-factors (-ox option),
and here i have problems.
I obtain a protein structure with a lot of errors :bonds and rings of LEU, GLU, GLN, PHE, PRO, ARG, TYR are abnormal.

I've used this command line:

g_rmsf -f traj.xtc -s file.tpr -n index.ndx -ox average.pdb

The average.pdb appears like this:
HEADER Protein in water

REMARK THIS IS A SIMULATION BOX

CRYST1 82.099 82.107 82.106 70.53 109.47 70.53 P 1 1

MODEL 1

ATOM 1 N THR A 1 102.438 58.760 45.270 1.00425.29

ATOM 2 H1 THR A 1 102.405 58.965 45.305 1.00483.72

ATOM 3 H2 THR A 1 102.369 59.009 45.257 1.00481.60

ATOM 4 H3 THR A 1 102.347 59.001 45.283 1.00477.17

ATOM 5 CA THR A 1 102.708 57.777 45.222 1.00325.73

ATOM 6 CB THR A 1 102.648 57.636 44.219 1.00332.12

Anyone can help me? There is something I can do?

Thanks in advance



#############
Andrea Carotti
Dip. Farmaco-chimico
Università di Bari
via E. Orabona, 4
CAP 70124
e-mail : and.carotti at farmchim.uniba.it
web: http://www.farmchim.uniba.it/samba/
phone: +39080/5442638
fax: +39080/5442230
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20030915/e1b5d481/attachment.html>