[gmx-users] [merge option in pdb2gmx
v.gogonea at csuohio.edu
Sun May 8 19:44:48 CEST 2005
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.
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
>> peptide). Is there a way to avoid this elimination of termini?
> yes, give the chains a different chain label.
>> Thank you for your help.
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
> 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
> gmx-users mailing list
> gmx-users at gromacs.org
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