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<DIV><FONT face=Arial size=2>Hi all<BR>I’m doing FEP calculation on Zn
ions.<BR>Is three a way to put position restraints <BR>on perturbated /
dummy atoms.<BR>When I define in my system.top:</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>…<BR>…<BR>#include "zn.itp"<BR>[
position_restraints ]<BR>; i funct
fcx
fcy fcz<BR>
1 1
1000
1000 1000</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>#include "cl.itp"<BR>[ position_restraints
]<BR>; i funct
fcx
fcy fcz<BR>
1 1
1000
1000 1000</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>#include "dum.itp"<BR>[ position_restraints
]<BR>; i funct
fcx
fcy fcz<BR>
1 1
1000
1000 1000</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>[ system ]<BR> .. <BR>…<BR>..</FONT></DIV>
<DIV> </DIV><FONT face=Arial size=2>
<DIV><BR>I’m perturbating Zn ions into dummy atoms. <BR> (I’m using ffgmx
I’ve added new DUM atomtype)<BR>When I use grompp I get following warning:</DIV>
<DIV> </DIV>
<DIV>..<BR>..<BR>checking input for internal consistency...<BR>calling
/lib/cpp...<BR>processing topology...<BR>Generated 1238 of the 2080 non-bonded
parameter combinations<BR>WARNING 1 [file "system.top", line 11]:<BR> No
default Position Rest. types for perturbed atoms, using normal values<BR>WARNING
2 [file "system.top", line 21]:<BR> No default Position Rest. types for
perturbed atoms, using normal values<BR>Excluding 3 bonded neighbours for
Protein 1<BR>turning H bonds into constraints...<BR>..<BR>..</DIV>
<DIV> </DIV>
<DIV>How can I apply position restraints on them. <BR>Please give me some
comment on this and thank you in advance!!<BR>All best.
<BR></FONT></DIV></BODY></HTML>