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<DIV><FONT face=Arial size=2>Back to my "old" good days, while a biochemist
student.</FONT></DIV>
<DIV><FONT face=Arial size=2>A resting human consumes about 40 Kg of ATP in 24
hours.</FONT></DIV>
<DIV><FONT face=Arial size=2>During heavy exercises, it could reach 0.5 Kg
/minute.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Regards.</FONT></DIV>
<DIV><FONT face=Arial size=2>Nuno</FONT></DIV></DIV>
<DIV>######################################<BR>Nuno Ricardo Santos Loureiro da
Silva Ferreira<BR>Departamento de Química<BR>Faculdade de Ciências e
Tecnologia<BR>Universidade de Coimbra<BR>3004-535 Coimbra - Portugal<BR>Fax:
+351 239 827703 - <A
href="http://www.biolchem.qui.uc.pt">www.biolchem.qui.uc.pt</A><BR>########################################</DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=kamilt@ibmb.uni.wroc.pl href="mailto:kamilt@ibmb.uni.wroc.pl">Kamil
Tamiola</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Monday, April 26, 2004 6:45
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] ATP and
Gromacs</DIV>
<DIV><BR></DIV>
<DIV>
<DIV><FONT face=Arial size=2>Well I've made a mistake and responded to the
wrong message.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Here is a small tip:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Please check your input file (ATP section)
and compare it with ffgmx.rtp topology file. It seems that You
will have to change the name of Your ATP atom PG to the name listed in
ffgmx.rtp. If You are not succesfull please try to reconstuct Your topology by
calculationg a new one . You can do it with <FONT color=#008000><A
href="http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html">http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html</A></FONT><FONT
color=#000000> ProdG server.</FONT></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>As for the hydrolysis, You will not be able to
simulate the phenomenum of ATP hydrolysis unless You use the quantum approach.
A typical MD can't simulate covalent bond formation. </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Good Luck </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Kamil</FONT></DIV></DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=sreeyapu@rediffmail.com href="mailto:sreeyapu@rediffmail.com">SLN
Prasad Reddy</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Monday, April 26, 2004 7:36
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] ATP and
Gromacs</DIV>
<DIV><BR></DIV>
<P><BR>Hi ,<BR> I am trying to run gromacs on a protein
having ATP.I started simulation with a command "pdb2gmx" and it is giving
following error<BR><BR>Fatal error: Atom PG in residue ATP 250 not found in
rtp database<BR> while sorting
atoms
<BR><BR>Please suggest me how to overcome
this. <BR><BR><BR><BR>Thank you<BR><BR>Prasad reddy <BR></P><BR><BR><A
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