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<DIV><FONT face=Arial size=2>Hello,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I am still a "kindergarten" user of GROMACS, but
already with serious troubles:</FONT></DIV>
<DIV><FONT face=Arial size=2>1)In the file ffgmx.rtp, we can read in the [
bondedtypes ] field that the dihedrals function is set to 1. But I do want to
use both 1 and 3 functions in my molecule (DPPC). In fact, even after
the [ dihedrals ] field of the [ DPPC ] molecule in the
ffgmx.rtp file has been written explicitly by me, with both 1 and
3 dihedral functions, the ??.top output of pdb2gmx program contained only
dihedrals of type 1 ! I have not forgotten to use the CP2, CP3 atom types in the
type 3 dihedrals.</FONT></DIV>
<DIV><FONT face=Arial size=2>Must I re-compile the program, after making such
modifications in the ??.rtp files ?</FONT></DIV>
<DIV><FONT face=Arial size=2>2)The program grompp complains that the angles in
the [ angles ] field of my ??.top (output of pdb2gmx) don't exist in the
ffgmx force field. Why ? I am surprised with that because the [ angles ]
field in the .rtp file is optional, and I only have to write it down,
should I want to override the .itp values.</FONT></DIV>
<DIV><FONT face=Arial size=2>Could anybody help me ?</FONT></DIV>
<DIV><FONT face=Arial size=2>Bye.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Pedro L.
Loureiro </FONT></DIV></FONT></DIV></BODY></HTML>