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<DIV><FONT face=Arial>Hi,</FONT></DIV>
<DIV><FONT face=Arial> I have a long md run of 1800
frames and I' ve seen that it's ok.</FONT></DIV>
<DIV><FONT face=Arial>Now I'm trying to analyze it with g_rmsf to obtain an
average structure with the b-factors (-ox option),</FONT></DIV>
<DIV><FONT face=Arial>and here i have problems.</FONT></DIV>
<DIV><FONT face=Arial>I obtain a protein structure with a lot of errors :bonds
and rings of LEU, GLU, GLN, PHE, PRO, ARG, TYR are abnormal.</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>I've used this command line:</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>g_rmsf -f traj.xtc -s file.tpr -n index.ndx -ox
average.pdb</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>The average.pdb appears like this:</FONT></DIV>
<DIV><FONT face=Arial><FONT size=2>
<P>HEADER Protein in water</P>
<P>REMARK THIS IS A SIMULATION BOX</P>
<P>CRYST1 82.099 82.107 82.106 70.53 109.47 70.53 P 1 1</P>
<P>MODEL 1</P>
<P>ATOM 1 N THR A 1 102.438 58.760 45.270 1.00425.29</P>
<P>ATOM 2 H1 THR A 1 102.405 58.965 45.305 1.00483.72</P>
<P>ATOM 3 H2 THR A 1 102.369 59.009 45.257 1.00481.60</P>
<P>ATOM 4 H3 THR A 1 102.347 59.001 45.283 1.00477.17</P>
<P>ATOM 5 CA THR A 1 102.708 57.777 45.222 1.00325.73</P>
<P>ATOM 6 CB THR A 1 102.648 57.636 44.219 1.00332.12</P>
<P><FONT size=3>Anyone can help me? There is something I can do?</FONT></P>
<P><FONT size=3>Thanks in advance</FONT></P></FONT></FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial></FONT><FONT face=Arial><BR>#############<BR>Andrea
Carotti<BR>Dip. Farmaco-chimico<BR>Università di Bari<BR>via E. Orabona,
4<BR>CAP 70124<BR>e-mail : <A
href="mailto:and.carotti@farmchim.uniba.it">and.carotti@farmchim.uniba.it</A><BR>web:
<A
href="http://www.farmchim.uniba.it/samba/">http://www.farmchim.uniba.it/samba/</A><BR>phone:
+39080/5442638<BR>fax: +39080/5442230</FONT></DIV></BODY></HTML>