[gmx-users] [merge option in pdb2gmx

David van der Spoel spoel at xray.bmc.uu.se
Sun May 8 21:00:08 CEST 2005

On Sun, 8 May 2005, Valentin Gogonea wrote:

>I really appreciate your help. I tried again, with no success. If the 
>topologies of the different chains are in separate itp files, then 
>where the bonding information about crosslinking is written? As far is 
>I noticed is not in top file.

Have you tried looking at the coordinates? There' isn't a single peptide 
bond here. There are just four cysteines. If you want this to work you'll 
have to use four different labels.

>Here is the command line that I have used:
>pdb2gmx -f zn4cys.pdb -o zn4cys.gro -p zn4cys.top -ff oplsaa -merge
>I attached here the pdb file and the specbon.dat file.
>Thank you again.

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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