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

[David van der Spoel]

On Mon, 2002-09-30 at 11:28, 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).
If you give them different labels pdb2gmx will be happy.
> 
> Terveisin, Markus
> 
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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