[gmx-users] regarding itp

[Mark Abraham]

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

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.