[gmx-users] Termini for a collection of fractions of protein in one pdb file

[K.A. Feenstra]

Markus O Kaukonen wrote:
> 
> Dear All,
> 
> I have a collection of pieces of protein in one pdb file
> (obtained by taking all atoms closer than xx au from iron and
> not breaking any amino acids.)
> 
> However, pdb2gmx only set correct termini (NH3+ or COO- in my case)
> to aminoacids that are at the beginning and in the end of the pdb file,
> and termini (of protein fractions) sitting in the middle of the
> pdb file are lef untouched (which is incorrect).
> 
> Question: Has someone coded a program that puts different pieces of
> protein in different pdb files or solved this problem by some other means?
> (Did not find this in the manual or FAQ).
> Or do I have to do it myself (breaking the protein by hand to various pdb
> files is too much for me).

pdb2gmx only (exclusively) uses chain-identifiers to determine which
parts of the .pdb file are one protein chain. In your case all your 
fragments probably have the same (or no) chain identifier, in which
case pdb2gmx will treat it as a single protein. The suggestion of 
David will fix this: add different chain identifiers to the different
non-contiguous fragments. This might or might not be more work than
putting them in separate files.

The reason it is like this, is that it this is a very straightforward
way of dealing with multiple chains, and you can change the identifiers
however you would like. A distance based criterion would be completely
automated, which makes it hard to let pdb2gmx make different choices.

Having said that, it would be nice to have the *option* in pdb2gmx to
use a distance based criterion for determining chain-breaks in the pdb
file. It would certainly be not too hard to put in (once you get to be
familiar with the 'structure' of the pdb2gmx code... ;-).


-- 
Groetjes,

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