[gmx-users] how to create itps of a ploymer

[K.A. Feenstra]

吴显辉 wrote:
>      
> All gmx-users
> 　   I am a novice of Gromacs. Now,my job is to study the dynamcis of a 
> ion channel.This channel is composed of esters.How can I create its 
> *.itp file?Should  I create a itp of monomer  or or all of ploymer?
>   Second, I think the amino acids' rtps are made from the coordinates of 
> Gly-X-Gly.Here X denotes the amino acid that we need to create its rtp 
> file. If  I want to create a ester's itp,shoud I calculate the 
> coordinates of ester-ester-ester.

The .rtp file has nothing to do with coordinates, it only
describes the system topology (connectivity, i.e. bonds,
angles, dihedrals) and atom properties (types and/or
mass and charges). But maybe you mean that the amino-acid
.rtp entries correspond to the residues, and not to the
isolated amino-acid molecules, in which case you are correct.


P.S. Personally, I prefer not to recieve the fancy type
of .html formatted e-mail you sent to the list (let alone
binary encoded). I'm sure there are many others on the
list that would agree...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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