[gmx-users] Incorrect C-terminal in peptide starting with GLY

[Krzysztof Kuczera]

Thank you
Krzysztof

Berk Hess wrote:
> Hi,
>
> I fixed it for the next beta release.
> If you need it now, change on line 1574 (my latest version) of 
> src/kernel/pdb2gmx.c
> cc->r_start to cc->r_end, or get the 4.5 version from git.
>
> Berk
>
> Date: Tue, 24 Aug 2010 09:21:44 -0500
> From: kkuczera at ku.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Incorrect C-terminal in peptide starting with GLY
>
> Hi gmx-users
> I am trying to set up a simulation of a 16-residue peptide that starts 
> with GLY and ends with GLU
> (PDB attached) using OPLS-AA/L and gromacs-4.5-beta3. Here is the 
> pdb2gmx command
>  
> pdb2gmx -inter -ignh -f b-hp41-56.pdb -p peptide.top -o peptide.gro
>  
> the ff, water, ionization state selection goes well,
>  I get a selection of N-terminals that includes GLY-NH3+ which is fine
> but then the selection of C-terminals does not have COO-, but only GLY-COO-
> - as a result the C-terminal GLU ends up with incorrect charge and qtot 
> is not an integer
>  
> Without the '-inter', the system gets GLY-NH3+ and GLY-COO- as well ...
>  
> Could someone suggest a fix for this ?
>  
> Regards
> Krzysztof
>  
> -- 
> Krzysztof Kuczera
> Departments of Chemistry and Molecular Biosciences
> The University of Kansas
> 2010 Malott Hall
> Lawrence, KS 66045
> Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
> http://oolung.chem.ku.edu/~kuczera/home.html <http://oolung.chem.ku.edu/%7Ekuczera/home.html>
>  
>  
>   
>
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-- 
Krzysztof Kuczera
Professor
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html