[gmx-users] [merge option in pdb2gmx

David van der Spoel spoel at xray.bmc.uu.se
Sun May 8 20:06:32 CEST 2005

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 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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