Ye Yang wrote:
Hi, Justin:
Thank you for the reply.
But I am not sure for gromacs 4.5.4. since for gromacs 3.3.1, I
only need one itp file for my forcefield. Should I just split this
forcefield.itp file into two different part, and write a new
forcefield.itp which says "#include ffnonbonded.itp, #included
ffbonded.itp"?
That's all the forcefield.itp file has ever done, really. It defines the
default interaction types for the system and #includes the relevant bonded and
nonbonded parameters. Maybe that's what your forcefield.itp file does, but in
the file listing, you did not have ffnonbonded.itp and ffbonded.itp. These
files are where grompp gets the bulk of its information and without them will be
hopelessly broken. All required input files are described in the manual, Chapter 5.
-Justin
Is there any suggestion how I can do that properly?
Thank you very much.
Ye
2011/8/18 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
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 <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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========================================
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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