[gmx-users] [merge option in pdb2gmx

[David van der Spoel]

On Sun, 8 May 2005, Valentin Gogonea wrote:

>To be concrete, I want to make a Cys-Zn-Cys bridge between two protein  
>chains. The Zn-Cys is modeled as a covalent bond. The two peptide  
>chains have different letters. If I use merge both peptides will be in  
>the top file and two termini will be removed and warning of too log  
>bonds are given.
>----
>Warning: Long Bond (26-28 = 0.574455 nm)
>Warning: Long Bond (51-53 = 0.565515 nm)
>----
>
>If the Zn atom is in the pdb file I get an error:
>----
>Linking ZN-1 ZN-1 and CYS-3 SG-14...
>Linking ZN-1 ZN-1 and CYS-4 SG-20...
>Linking ZN-1 ZN-1 and CYS-5 SG-26...
>Linking ZN-1 ZN-1 and CYS-6 SG-32...
>There are 7 donors and 7 acceptors
>There are 7 hydrogen bonds
>Checking for duplicate atoms....
>No N- or C-terminus found: this chain appears to contain no protein
>Fatal error: Atom -C not found in residue THR2 while adding hydrogens
>-----
>Thank you for suggestion.

Something else is wrong with your file or the options you're using.
If you label the complete first chain A and the second B you will get two 
topologies with two termini each. This also works with the merge option, 
since that was created exactly for the purpose of crosslinking protein 
chains. Check the -ter and -ignh options. If you can't make it work please 
send me the pdb file and the specbond.dat file.


 -- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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