Send a copy of your ffgmx.n2t, ffgmxbon.itp, and SWNT_6_6_144.pdb files
please, if the following does not work. Also I think that the information
updated in ffgmxbon.itp might be found in a different file with the 3.3.3
version (I think from looking at previous e-mails that it is
ffencadvbon.itp). If any one could let me know I will make an addendum to my
site for this new version. (I am about done using GROMACS due to the fact
that I am graduating, so I will not be updating mine)
~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Hero
Sent: Wednesday, April 23, 2008 5:44 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] x2top error in CNT simulation on Gromacs 3.3.3
Dear All,
I am trying to simulate water flow in CNT and just followed the website:
http://cs86.com/CNSE/SWNT.htm
I did the following:
1. ffgmx.n2t
must change this files name to ffencadv.n2t and add the following 2
lines:
C C 1 C ; CNT Carbon with one bond
C C 2 C C ; CNT double bonded Carbon
2. ffgmxbon.itp
add the following line to it:
#
[ bondtypes ]
; i j func b0 kb
C C 1 0.14210 478900.
#
[ angletypes ]
; i j k func th0 cth
C C C 1 120.000 397.480
#
[ dihedraltypes ]
; i l func q0 cq
C C 1 0.000 167.360
#
But when I ran:
x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp
Error message appeared:
Can not find forcefield for atom C-1 with 2 bonds
.
Can not find forcefield for atom C-143 with 2 bonds
Can not find forcefield for atom C-144 with 2 bonds
---
Program x2top, VERSION 3.3.3
Source code file: x2top.c, line: 206
Fatal error:
Could only find a forcefield type for 0 out of 144 atoms
---
Could you please tell me what is the problem? This works on Gromacs 3.3.1
Thank you very much!
Jue
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