Hi,
If you are using any of the united atom GROMOS96 forcefields then there is
already an rtp entry for ATP. Check out the .rtp files in the top folder.
All you need to do is to have the ATP atoms in the pdb file the same as the
atom names in the .rtp file for pdb2gmx to do all the work for you. If you
are not using a united atom forcefield then you will have to get your
parameters for ATP from somewhere else (or calculate them yourself - not
easy).
Hope this helps
Tom
--On Thursday, August 09, 2007 10:03:30 +0200 Maik Goette
<[EMAIL PROTECTED]> wrote:
Be aware, that you can't use the ouput with every forcefield...
Attaching the gro-file to your protein gro at the proper position (right
after the protein) and building the correct topology should do the job.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
mjduan wrote:
Yes, I found a server (ProDrg) can get the .gro and .top files of ATP
molecule.
---------------------------
Whereas one should also mention, that ATP isn't included in every
forcefield, GROMACS supports...
So probably, parameterization has to be done also.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Mark Abraham wrote:
mjduan at smail.hust.edu.cn wrote:
Dear GROMACS users:
I want to simulate a complex composed by a protein and an ATP
molecule, and when I use the pdb2gmx to build the topology file and
transfer the*pdb* file to *gro* file, it said "/Fatal error: Atom PG
in residue ATP 1 not found in rtp entry with 36 atoms while sorting
atoms/", So how can I build the *top* file and *gro* file for ATP
molecular and simulate the protein molcular and ATP molecule
simultaneity?
By reading chapter 5 of the manual thoroughly, understanding how the rtp
files work for your force field and modifying your .pdb file and/or
force field files to work suitably.
Mark
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TJ Piggot
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University of Bristol, UK.
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