<div dir="ltr">Hi, everyone:<br> I am using a forcefield PACE(modified) from my friends.<br> 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.<br>
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.<br>
However, I met the same problem of "atomtype Nr not found each time". It is the N of Arg in this force field<br> 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.). <br>
The folders PACE_13_NAMD.ff/ has the following files:<br> aminoacids.c.tdb aminoacids.n.tdb atomtypes.atp forcefield.itp<br>aminoacids.ddb aminoacids.r2b cg216water.gro watermodels.dat<br>aminoacids.hdb aminoacids.rtp cgWater.itp<br>
<br><br> I already included the itp file in the top file:<br><br>in the top file, it indeed has:<br><br> ; Include forcefield parameters<br>#include "PACE_13_NAMD.ff/forcefield.itp"<br><br>Also in the forcefield.itp file, it has:<br>
<br>Nr 16.000 0.000 A 0.0 0.0<br><br>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).<br>
<br>Right now, I am really confused what is going on, could someone please help me with this?<br><br>Thank you very much.<br><br>Best<br>Wishes<br><br>Ye<br><br><br><br></div>