<div dir="ltr">Oh, I see it now.<br>
Even if I include all the needed terms in one file forcefield.itp, I
need to create files separated, using file name ffnonbonded.itp and
ffbonded.itp?<br>
Thank you very much<br>
<br>
Ye<br><br><div class="gmail_quote">2011/8/18 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><br>
<br>
Ye Yang wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi, Justin:<br>
Thank you for the reply.<br>
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"?<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div>
Is there any suggestion how I can do that properly?<br>
Thank you very much.<br>
<br>
Ye<br>
<br></div>
2011/8/18 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div><div></div><div><br>
<br>
<br>
<br>
Ye Yang wrote:<br>
<br>
Hi, everyone:<br>
I am using a forcefield PACE(modified) from my friends.<br>
Since there was a small program generating some dihedral<br>
terms based on gromacs3.3.1, I need to use gromacs 3.3.1 to<br>
generate the gromacs file.<br>
Previously, for the npt/nvt, I was also using grompp (gromacs<br>
3.3.1) to generate the simulation file and run it in gromacs<br>
4.5.4, it works perfectly. However, I met some problem: since<br>
the pulling (constant velocity or force)in gromacs 3.3.1 is<br>
totally different from gromacs 4.5.4, I cannot use the same<br>
method, so I turned to grompp 4.5.4.<br>
However, I met the same problem of "atomtype Nr not found<br>
each time". It is the N of Arg in this force field<br>
I have already created the folder in the<br>
/home/yy58/gromacs/share/__<u></u>gromacs/top folder and tried gmx2pdb<br>
in gromacs 4.5.4, which can create the gro file and top file (so<br>
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.__<u></u>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<br>
definition of Nr also exists correctly (I have checked it and<br>
also use grompp to run it in gromacs3.3.1, which does not have<br>
any trouble).<br>
<br>
Right now, I am really confused what is going on, could someone<br>
please help me with this?<br>
<br>
<br>
You are missing the ffnonbonded.itp and ffbonded.itp files, which<br>
causes your force field to break. The ffnonbonded.itp file is the<br>
source of this particular error, since that is where grompp looks to<br>
find the nonbonded parameters for each atom type (among other things).<br>
<br>
-Justin<br>
<br>
-- ==============================<u></u>__==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
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-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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