[gmx-users] Protein Simulations using gromacs

Komath Damodaran kdamodaran at telik.com
Thu Nov 2 17:48:19 CET 2006

Hi all,

I have couple of basic questions:

1. Is there an option in pdb2gmx to retain the original residue numbers?

2. What is the common practice to deal with breaks in the protein
chains? Is it good to terminate each fragment with acetyl groups?





Komath Damodaran

Scientist, Computational Chemistry

Telik, Inc.

3165 Porter Drive

Palo Alto, CA 94304

Tel: (650) 845-7838, Fax: 650-845-7800


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