[gmx-users] .rtp files
David van der Spoel
spoel at xray.bmc.uu.se
Sat Sep 8 16:04:15 CEST 2001
On Sat, 8 Sep 2001, Pedro Loureiro wrote:
>I am still a "kindergarten" user of GROMACS, but already with serious troubles:
>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.
>Must I re-compile the program, after making such modifications in the ??.rtp files ?
Check out Peter Tielemans homepage (see link on gromacs.org)
He has the topologies online.
Also when you change the topologies you don't have to recompile.
>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
The values have to come from somewhere. If you don't specify them in the
rtp file they have to come from the other part of the force field which in
this case is the ffgmxbon.itp file.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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