Ye Yang wrote:
Hi, everyone:
I am using a forcefield PACE(modified) from my friends.
Since there was a small program generating some dihedral terms
based on gromacs3.3.1, I need to use gromacs 3.3.1 to generate the
gromacs file.
Previously, for the npt/nvt, I was also using grompp (gromacs 3.3.1)
to generate the simulation file and run it in gromacs 4.5.4, it works
perfectly. However, I met some problem: since the pulling (constant
velocity or force)in gromacs 3.3.1 is totally different from gromacs
4.5.4, I cannot use the same method, so I turned to grompp 4.5.4.
However, I met the same problem of "atomtype Nr not found each
time". It is the N of Arg in this force field
I have already created the folder in the
/home/yy58/gromacs/share/gromacs/top folder and tried gmx2pdb in gromacs
4.5.4, which can create the gro file and top file (so as I see, it seems
the adding of the force field is correct.).
The folders PACE_13_NAMD.ff/ has the following files:
aminoacids.c.tdb aminoacids.n.tdb atomtypes.atp forcefield.itp
aminoacids.ddb aminoacids.r2b cg216water.gro watermodels.dat
aminoacids.hdb aminoacids.rtp cgWater.itp
I already included the itp file in the top file:
in the top file, it indeed has:
; Include forcefield parameters
#include "PACE_13_NAMD.ff/forcefield.itp"
Also in the forcefield.itp file, it has:
Nr 16.000 0.000 A 0.0 0.0
Similarly, in the file atomtypes.atp, aminoacids.rtp, the definition of
Nr also exists correctly (I have checked it and also use grompp to run
it in gromacs3.3.1, which does not have any trouble).
Right now, I am really confused what is going on, could someone please
help me with this?
You are missing the ffnonbonded.itp and ffbonded.itp files, which causes your
force field to break. The ffnonbonded.itp file is the source of this particular
error, since that is where grompp looks to find the nonbonded parameters for
each atom type (among other things).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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