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<DIV><FONT face=Arial size=2>Hi all.<BR>1)</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>Thank you all for comments and help on FEP
issue. <BR> I still have problems with setting up the system. <BR>How can
I obtain topology for DPPC lipids to use with GROMOS96 <BR>force field for
protein membrane simulations. Should I <BR>stay with old ffgmx force
field, is it the best choice.<BR>Is it possible to adopt old lipid parameters
(lipid.itp<BR> for ffgmx) for new GROMS96 force field. </FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>2)</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>During FEP calculations I need to <BR>slowly turn
off charges and LJ interactions for Zn2+ ion.<BR>In my dual topology for Zn2+ I
have:</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2> <BR>[ moleculetype ]<BR>;
molname
nrexcl<BR>ZnB
1</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>[ atoms ]<BR>; id at type res
nr residu name at name cg nr
charge
typeB chargeB massB<BR>1
Zn 1
Zn
Zn 1
2 65.37000 Zn
(?) 0 0</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>and that will only perturbate charges on the Zn
atom. <BR> In order to turn off Zn ion LJ interactions I need
to <BR>change it into dummy atom. I’m using ffgmx forcefield
and<BR> which atom type should I use for above Zn(?). I checked
<BR>ffgmx.atp and there is no atom type DUM (like in GROMOS96).
<BR> Does it mean I have to add new atom type DUM in all
ffgmx.atm,<BR> ffgmxnbon.itp…. files. Please give my some
suggestions. <BR>Thank you for your time and help.<BR>All
best.</FONT></DIV></BODY></HTML>