[gmx-users] [merge option in pdb2gmx
v.gogonea at csuohio.edu
Mon May 9 16:42:22 CEST 2005
I finally got it right by making the Zn ion part of one of the 4 chains
and not treat it as a separate chain.
Thank you for the help.
On May 8, 2005, at 3:00 PM, David van der Spoel wrote:
> 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
> bond here. There are just four cysteines. If you want this to work
> 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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