[gmx-users] merge option in pdb2gmx

David van der Spoel spoel at xray.bmc.uu.se
Sun May 8 18:41:24 CEST 2005

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.
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>gmx-users at gromacs.org
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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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