[gmx-users] Nterm acetyl cap
spoel at xray.bmc.uu.se
Fri Oct 14 08:25:01 CEST 2005
On Thu, 2005-10-13 at 22:00 -0400, deepa rajamani wrote:
> How do I take care of acetyl cap of Nterm in the MD simulation of protein
> in water. The ACE group is not recognized by GROMACS.
> Do I have to manually make the topology and give the connecting bonds?
Unfortunately the names of residue and atoms differ between force
fields. Please check the rtp file of the force field you want to use and
then rename the atoms and residue in your pdb file accordingly.
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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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