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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