Hi,
I missed one dash in the front. So it should be
include = -IffG43b1.n2t
The problem you had was because of improper usage of include, for every item to
be put in include=, you shall prefix -I in the front. Since you have not put
it, cpp couldn't finish parsing the topology file, so your topology contains
nothing.
ffG43b1.n2t is not necessary for grompp.
You shall include spc.itp in your topology file to include the topology for
water. So your file header shall be like
#include "ffG43b1.itp"
#include "spc.itp"
Last and most important, the line you added to ffgmxbon.itp is useless because
you are using GROMOS96 force field.
So you shall change ffG43b1.itp to ffgmx.itp. And add the line
C C 1 0.14210 478900.
To the end of section [ bondtypes ], not the end of the whole file.
So the command line without -maxwarn can work properly. Note that you shall not
use -maxwarn in most cases.
grompp -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p
SWNT_6_6_144_post_genbox.top -pp
The suffix _s is just what I have specified for my build. You don't need the
same setting.
Regards,
Yang Ye
On 7/25/2007 10:29 PM, Christopher Stiles wrote:
Yang,
Thank you very much for you help. I am sorry I did not think to package my
files and commands up I will do so by the end of the day. As to the
ffG43b1.n2t it was to get x2top to work, it defines single and double bonded
carbon so that I do not have to cap my tube with hydrogen. Although I am not
sure how you got the include to work with:
include = IffG43b1.n2t
Do you have a file named IffG43b1.n2t in your lib or your working dir?
The file comes from the ffgmx.n2t file in the Gromacs lib but the name is
changes to ffG43b1.n2t and the following 2 lines are added:
C C 1 C ; CNT Carbon with one bond
C C 2 C C ; CNT double bonded Carbon
Next must I use grompp_s? (I believe this is grompp with single accuracy,
correct?) Because if so I will have to compile it.
Last question, by it gives a pass do you mean you get a little over 1500
warnings and then get the following:
Fatal error:
No such moleculetype SOL
Thank you so much for your help I really appreciate it,
~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA
Hi,
Sorry that most of us on the list were too busy to read one full page of
details and download individual files. We might just prefer to download
one package, and run a script file for us quickly dive into the problem.
Is include in mdout_test.mdp a standard option? Where did you get it? I
changed it to
include = IffG43b1.n2t
It works. Otherwise, cpp terminates before it generates a full top.
grompp -pp is always a good friend for grompp error (and thorough
reading of chapter 5 of manual).
Next issue comes the format of ffG43b1.n2t. I don't think it conforms to
any GROMACS topology format. Again where does it comes from?
My grompp command line:
grompp_s -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p
SWNT_6_6_144_post_genbox.top -maxwarn 10000000 -pp
It gives a pass, at least.
Hope you can work further on.
Regards,
Yang Ye
On 7/25/2007 2:41 AM, Christopher Stiles wrote:
I am trying to simulate a single wall carbon nanotube in a box
solvated in water, at 300k for about 200ps. Also once I accomplish
this I wish to fix either one end of the tube or fix the center of
mass position, although this part is unimportant if I can not get the
thing to run at all yet.
I have created a page with a full detailed account of what I have done
and tried so far. http://cs86.com/CNSE/SWNT.htm
Please note all files where created with Vim in the unix environment
so I think I have eliminated the formatting issues.
Also that I have tried the simulation with many different sized tubes
from TubeGen (http://turin.nss.udel.edu/research/tubegenonline.html ),
both with and without hydrogen capped ends (this is something I have
read in the archives as a possible solution, it makes no difference in
the end).
I have come to the conclusion through the help of many of you that the
*.pdb file from TubeGen and mainly the residue UNK among other
things. If any one has had luck with using a TubeGen file to create a
simulation please let me know as to how. Other wise I am looking at a
few new options basically all of them involve writing my own files.
I guess I am looking for advice where to go from here.
~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA
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