On 12/21/2011 5:53 PM, priya thiyagarajan wrote:
hello sir,
thanks for your reply..
sorry for disturbing you again and again..
i understood that i need to add my residue BFC in my rtp file and
residuetype.dat file.
i like to clarify one thing.
i added BFC as lipid in my residuetypes.dat file.
then i need to include my residue BFC in .rtp file.
To add in that rtp file i need itp file for my fattyacid. so that can
use those atomtypes dihedrals in my rtp.
am i correct..
pdb2gmx uses the .rtp entries to construct a [moleculetype], as you
already know from your reading of chapter 5 (particularly section 5.6)
of the manual... right? A molecule .itp file already contains a
[moleculetype]. Both of those need to either declare their function
parameters on the line that uses them, or rely on grompp to later look
them up from the atom types in the force field .itp files. So you need
either to map the atoms in your BFC to the pre-defined atomtypes so that
the existing parameters can be looked up, or you need to develop the
parameters yourself (which would be a bad idea at what appears to be
your current level of experience).
Mark
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