[gmx-users] peptide attached with a linker

David spoel at xray.bmc.uu.se
Sat Apr 9 19:37:23 CEST 2005

On Sat, 2005-04-09 at 21:18 +0530, purohit at iitk.ac.in wrote:
> Hi gromacs users
>    I am trying to simulate a decapeptide where two pentapeptide are
> connected by a short alkyl linker. how can i get the pdb file for this.
> can i use the prodrug server in some way ?
That might work, but it limits you to the GROMOS force field. The
alternative is to edit force field files of your choice (rtp, hdb,
specbond.dat). Search the list for tips.

> thanking you in advance.
> Chandra Shekhar Purohit
> Ph.D student
> C/O. Dr. Sandeep Verma
> Dept. of Chemistry,
> Indian Institute of Technology-Kanpur
> Kanpur-208016
> India.
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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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