<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV></DIV>
<DIV>Dear GROMACS users and developers,</DIV>
<DIV> </DIV>
<DIV>Sorry for posting same topic again. I really appreciate those replies, thank you. I did use the -res option so i can get the plot rmsf (nm) vs residue. However, with -res option, the bfac.pdb produced include the ANISOU line for each atom (whish is the anistropic temperature factor). The B-factor is still at the end of each atom line.</DIV>
<DIV> </DIV>
<DIV>My question is, how can I calculate the average of each residue? here's few line i took form the bfac.pdb:</DIV>
<DIV> </DIV><SPAN lang=PT-BR style="mso-ansi-language: PT-BR">
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New" size=2>TITLE<SPAN style="mso-spacerun: yes"> </SPAN>Protein in water<BR>REMARK<SPAN style="mso-spacerun: yes"> </SPAN>THIS IS A SIMULATION BOX<BR></FONT><SPAN lang=SV style="mso-ansi-language: SV"><FONT face="Courier New" size=2>CRYST1<SPAN style="mso-spacerun: yes"> </SPAN>90.072<SPAN style="mso-spacerun: yes"> </SPAN>90.010<SPAN style="mso-spacerun: yes"> </SPAN>90.061<SPAN style="mso-spacerun: yes"> </SPAN>70.58 109.50<SPAN style="mso-spacerun: yes"> </SPAN>70.49 P 1<SPAN style="mso-spacerun: yes"> </SPAN>1<BR>MODEL<SPAN style="mso-spacerun: yes"> </SPAN>1<BR>ATOM<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>N<SPAN
style="mso-spacerun: yes"> </SPAN>ALA<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>39.870<SPAN style="mso-spacerun: yes"> </SPAN>49.598<SPAN style="mso-spacerun: yes"> </SPAN>31.575<SPAN style="mso-spacerun: yes"> </SPAN>1.00<SPAN style="mso-spacerun: yes"> </SPAN>0.00<BR></FONT></SPAN><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><FONT face="Courier New" size=2>ANISOU<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>N<SPAN style="mso-spacerun: yes"> </SPAN>ALA<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>27382<SPAN style="mso-spacerun: yes"> </SPAN>16872<SPAN style="mso-spacerun: yes"> </SPAN>28413<SPAN style="mso-spacerun: yes"> </SPAN>-5818 -15784<SPAN
style="mso-spacerun: yes"> </SPAN>-6247<BR>ATOM<SPAN style="mso-spacerun: yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> </SPAN>H1<SPAN style="mso-spacerun: yes"> </SPAN>ALA<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>40.270<SPAN style="mso-spacerun: yes"> </SPAN>50.118<SPAN style="mso-spacerun: yes"> </SPAN>30.815<SPAN style="mso-spacerun: yes"> </SPAN>1.00<SPAN style="mso-spacerun: yes"> </SPAN>0.00<BR>ANISOU<SPAN style="mso-spacerun: yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> </SPAN>H1<SPAN style="mso-spacerun: yes"> </SPAN>ALA<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>36121<SPAN style="mso-spacerun: yes"> </SPAN>21080<SPAN style="mso-spacerun: yes"> </SPAN>32250<SPAN
style="mso-spacerun: yes"> </SPAN>-8317 -17149<SPAN style="mso-spacerun: yes"> </SPAN>-8021<BR>ATOM<SPAN style="mso-spacerun: yes"> </SPAN>3<SPAN style="mso-spacerun: yes"> </SPAN>H2<SPAN style="mso-spacerun: yes"> </SPAN>ALA<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>40.080<SPAN style="mso-spacerun: yes"> </SPAN>48.628<SPAN style="mso-spacerun: yes"> </SPAN>31.485<SPAN style="mso-spacerun: yes"> </SPAN>1.00 221.02<BR>ANISOU<SPAN style="mso-spacerun: yes"> </SPAN>3<SPAN style="mso-spacerun: yes"> </SPAN>H2<SPAN style="mso-spacerun: yes"> </SPAN>ALA <SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>32407<SPAN style="mso-spacerun: yes"> </SPAN>19879<SPAN style="mso-spacerun:
yes"> </SPAN>31690<SPAN style="mso-spacerun: yes"> </SPAN>-6481 -17864<SPAN style="mso-spacerun: yes"> </SPAN>-7202</FONT></SPAN></P><SPAN lang=PT-BR style="mso-ansi-language: PT-BR">
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><FONT face="Courier New" size=2>ATOM<SPAN style="mso-spacerun: yes"> </SPAN>4<SPAN style="mso-spacerun: yes"> </SPAN>H3<SPAN style="mso-spacerun: yes"> </SPAN>ALA<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>38.870<SPAN style="mso-spacerun: yes"> </SPAN>49.728<SPAN style="mso-spacerun: yes"> </SPAN>31.575<SPAN style="mso-spacerun: yes"> </SPAN>1.00 218.06<BR>ANISOU<SPAN style="mso-spacerun: yes"> </SPAN>4<SPAN style="mso-spacerun: yes"> </SPAN>H3<SPAN style="mso-spacerun: yes"> </SPAN>ALA<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>33154<SPAN style="mso-spacerun: yes"> </SPAN>18573<SPAN
style="mso-spacerun: yes"> </SPAN>31125<SPAN style="mso-spacerun: yes"> </SPAN>-6794 -16678<SPAN style="mso-spacerun: yes"> </SPAN>-6289<BR>ATOM<SPAN style="mso-spacerun: yes"> </SPAN>5<SPAN style="mso-spacerun: yes"> </SPAN>CA<SPAN style="mso-spacerun: yes"> </SPAN>ALA<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>40.500<SPAN style="mso-spacerun: yes"> </SPAN>50.098<SPAN style="mso-spacerun: yes"> </SPAN>32.805<SPAN style="mso-spacerun: yes"> </SPAN>1.00 168.66<BR>ANISOU<SPAN style="mso-spacerun: yes"> </SPAN>5<SPAN style="mso-spacerun: yes"> </SPAN>CA<SPAN style="mso-spacerun: yes"> </SPAN>ALA<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>17671<SPAN style="mso-spacerun:
yes"> </SPAN>18590<SPAN style="mso-spacerun: yes"> </SPAN>27822<SPAN style="mso-spacerun: yes"> </SPAN>-3239 -12795<SPAN style="mso-spacerun: yes"> </SPAN>-8333<BR>ATOM<SPAN style="mso-spacerun: yes"> </SPAN>6<SPAN style="mso-spacerun: yes"> </SPAN>CB<SPAN style="mso-spacerun: yes"> </SPAN>ALA<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>39.990<SPAN style="mso-spacerun: yes"> </SPAN>49.098<SPAN style="mso-spacerun: yes"> </SPAN>33.845<SPAN style="mso-spacerun: yes"> </SPAN>1.00 220.77<BR>ANISOU<SPAN style="mso-spacerun: yes"> </SPAN>6<SPAN style="mso-spacerun: yes"> </SPAN>CB<SPAN style="mso-spacerun: yes"> </SPAN>ALA<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>15699<SPAN
style="mso-spacerun: yes"> </SPAN>36171<SPAN style="mso-spacerun: yes"> </SPAN>32009 -10813<SPAN style="mso-spacerun: yes"> </SPAN>-7176 -10100</FONT><BR></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt">Can I just average the (B-factor) value at each end of atom line for each residue? </P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"> </P>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt">Its okay if the B-factor vs redisue plot cant be build. I can use the B-factor vs atoms plot. But people (in papers) have done it (B-fac vs res) before with GROMACS and I'm eager to see the plot for my protein :) <BR></P>
<DIV></SPAN></SPAN>Comments, advices and suggestions are greatly appreciated. Thank You.</DIV>
<DIV> </DIV>
<DIV>"May the Force Fields be with You" - GROMACS Wars<BR> </DIV>
<P> </P>
<P>Muhammad Alif Mohammad Latif</P>
<DIV></DIV><BR>
<DIV>Department of Chemistry<BR>Faculty of Science<BR>Universiti Putra Malaysia<BR>43400 UPM Serdang, Selangor<BR>MALAYSIA
<DIV></DIV></DIV></div><br>
<hr size=1>Be a better friend, newshound, and
know-it-all with Yahoo! Mobile. <a href="http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ "> Try it now.</a></body></html>