I finally managed to cap it with hydrogen and I don't get any errors
now. It seems I had a wrong bond-length at the beginning. Thanks guys
for your your help :)
George
Robert Johnson wrote:
Do you want to simulate an infinite nanotube or a finite one?
Bob
On 3/28/07, George Abadir <[EMAIL PR
A finite one.
Thanks alot,
George
Robert Johnson wrote:
Do you want to simulate an infinite nanotube or a finite one?
Bob
On 3/28/07, George Abadir <[EMAIL PROTECTED]> wrote:
There is no C1 and C2 atom in the input PDB file, and the topology file
is not generated because x2top doesn't genera
Do you want to simulate an infinite nanotube or a finite one?
Bob
On 3/28/07, George Abadir <[EMAIL PROTECTED]> wrote:
There is no C1 and C2 atom in the input PDB file, and the topology file
is not generated because x2top doesn't generate a topology because of
the errors. I don't understand what
There is no C1 and C2 atom in the input PDB file, and the topology file
is not generated because x2top doesn't generate a topology because of
the errors. I don't understand what C (1) and C (2) means but it is not
C1 and C2; I mean not two different types of atoms. The PDB file is
generated sim
George Abadir wrote:
Hi, thank you very much for your help.
I capped the CNT with hydrogen atoms (i.e., I changed the carbon atoms
at the ends of the tube into hydrogen atoms), but now I get an error "No
forcefield type for atom C(1) with 2 bonds" instead of ""No forcefield
type for atom C(2) w
Hi, thank you very much for your help.
I capped the CNT with hydrogen atoms (i.e., I changed the carbon atoms
at the ends of the tube into hydrogen atoms), but now I get an error "No
forcefield type for atom C(1) with 2 bonds" instead of ""No forcefield
type for atom C(2) with 1 bonds" ! Is ther
Thank you very much for your reply.
I have added a couple of lines in the ffgmx.n2t file :" CC1
C (for the C atom with 1 bond)
CC 2 C C (for the C atom with 2 bonds)
I also changed the ffgm
When using x2top with a specific force field, things are assumed about
the connectivity of the molecule. The terminal carbon atoms of your NT
will only be bonded to, at most, 2 other carbons. In your case, it
looks like they are only bonded to one. When x2top tries to find the
forcefield associate
Hi,
I added CNT residue in the ffgmx.rtp as follows:
" [ CNT ]
[ atoms ]
C C0.00 0"
Then I used x2top to gene
Hi,
Actually, I believe that only one force field (ffgmx) currently has an
n2t file, at least as recently as 3.3.1. I would try running a find or
locate command to see if you even have the n2t files to begin with. I also
believe I read earlier on the mailing list that the CVS branch has some
im
George Abadir wrote:
Hi,
I am using Tubegen to generate a PDB file for carbon nanotubes. When
I use the "x2top" command I get an error :"Library file ffG43a1.n2t not
found in current dir nor in default directories". The same error is
repeated with every other force field. Where can I find
Hi,
I am using Tubegen to generate a PDB file for carbon nanotubes.
When I use the "x2top" command I get an error :"Library file ffG43a1.n2t
not found in current dir nor in default directories". The same error is
repeated with every other force field. Where can I find this file or how
can
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