[gmx-users] dialanine

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jun 9 07:46:27 CEST 2006

Hi Debashis,

Parameters and .pdb file are different things. To generate a structure for
dialanine you can use prodrg, pymol, write it by hand or search the web. If
you want to use your own force field parameters you have to write a .itp
file. Check the gromacs manual for that.


On 6/8/06, Debashis Dutta <ddutta at email.unc.edu> wrote:
> Hi,
>        I am seeking help in creating the .pdb file for a dialanine
> molecule using the databank. I have the parameters for a single alanine
> molecule. how do i go from here.
> Thanks
> Debashis
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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