[gmx-users] [merge option in pdb2gmx

[Valentin Gogonea]

David,

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.

Valentin

On May 8, 2005, at 3:00 PM, David van der Spoel wrote:

> On Sun, 8 May 2005, Valentin Gogonea wrote:
>
>> David,
>>
>> 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.
>>
>> Valentin
>>
>>
>
> --  
> 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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