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?
Thank you very much.
Best
Wishes
Ye
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