[gmx-users] [merge option in pdb2gmx

Valentin Gogonea v.gogonea at csuohio.edu
Sun May 8 20:31:46 CEST 2005


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.

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.


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On May 8, 2005, at 2:06 PM, David van der Spoel wrote:

> 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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