[gmx-users] x2top error in CNT simulation on Gromacs 3.3.3

Christopher Stiles CS145331 at albany.edu
Thu Apr 24 04:27:57 CEST 2008


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: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>On Behalf Of Hero
>Sent: Wednesday, April 23, 2008 5:44 PM
>To: gmx-users at 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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