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.
Tsjerk
On 6/8/06, Debashis Dutta <[EMAIL PROTECTED]> 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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