Ye Yang wrote:
Oh, I see it now.
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?
The #include keyword literally means "copy and paste the contents of this file
here." If those files don't exist, then nothing gets copied and you're missing
all of the parameters from the force field.
-Justin
Thank you very much
Ye
2011/8/18 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
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> <mailto: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> <http://vt.edu> | (540)
231-9080 <tel:%28540%29%20231-9080>
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/justin>
<http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
==============================____==========
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
<http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>>
Please search the archive at
http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>
<http://www.gromacs.org/__Support/Mailing_Lists/Search
<http://www.gromacs.org/Support/Mailing_Lists/Search>> before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-request@__gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read
http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>
<http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>>
--
==============================__==========
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>
==============================__==========
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
<http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
