[gmx-users] pdb2gmx and itp files

[Lubos Vrbka]

hi guys!

i'm a newbie to gromacs. i went through the manual (epsecially the 
section 5) and also the archives and one thing still remains a mystery 
to me.

i know that pdb2gmx can be used to convert pdb file to topology. from 
what i've learned it seems to me that it is capable of doing this task 
for residues it knows from the appropriate forcefield .rtp file.

in the manual, it is written, that there is a possibility to add new 
residue to .rtp file, however:

(quote from manual - page 93)
It is better not to change this file because it is standard input for 
pdb2gmx, but if changes are needed make them in the *.top file (see 
5.6.1). However, in the ff???.rtp file the user can define a new 
building block or molecule: see for example 2,2,2-trifluoroethanol (TFE) 
or n-decane (C10). But when defining new molecules (non-protein) it is 
preferable to create a *.itp file.
(end quote from manual)

i create molecular .itp file for some substance (e.g. urea, like in the 
manual). it seems that this file cannot be used in pdb2gmx to help 
converting pdb to .top and .gro files. is it really so? is the only way 
how to enable this to create my own forcefield (.atp, .rtp, and other 
files)?

thank you for your help,

-- 
Lubos
_ at _"