[gmx-users] [merge option in pdb2gmx

[Valentin Gogonea]

David,

Thank you for your answer, but unfortunately I could not solve the  
problem with your suggestion.

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.


Valentin

Begin forwarded message:

> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Date: May 8, 2005 12:41:24 PM EDT
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] merge option in pdb2gmx
> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> On Sun, 8 May 2005, Valentin Gogonea wrote:
>
>> GMX users,
>>
>> I am trying to make a bridge between two peptide chains using the
>> specbond.dat file. It works only if the "merge" option in the pdb2gmx
>> is used, but in this case pdb2gmx creates a bond between the two
>> peptide chains which eliminates two of the chain termini (one from  
>> each
>> peptide). Is there a way to avoid this elimination of termini?
> yes, give the chains a different chain label.
>
>>
>> Thank you for your help.
>>
>> Valentin
>>
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>
> --  
> 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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