[gmx-users] RE: x2top error in CNT simulation on Gromacs 3.3.3 (Christopher Stiles)

[Christopher Stiles]

Jue,
     Please read over this wiki article that I sent to you just the other
day: http://wiki.gromacs.org/index.php/Carbon_Nanotube
Please to special note of the sending e-mails to the mailing list and not
individuals, while then every one can benefit. On my site I set it up so
that you can check to make sure you are doing things correctly every step of
the way by providing copies of files that you should have at each step and a
complete copy of my output with each step. Please take some time to learn
how *.pdb file should look like and its format.

Since I do not have version 3.3.3 I can not really offer any better advice.

Take care,
~Christopher Stiles

>-----Original Message-----
>From: Hero [mailto:cjt0610 at yahoo.com]
>Sent: Thursday, April 24, 2008 12:42 PM
>To: CS145331 at albany.edu
>Subject: x2top error in CNT simulation on Gromacs 3.3.3 (Christopher
>Stiles)
>
>Dear Mr. Stiles,
>
>Thank you so much for your reply!
>
>Sorry I keep on bugging you on CNT! But I do have problems making it
>run on Gromacs 3.3.3.
>
>I have spent a lot of time trying to figure out the problems, unfortunately
>I still do not know what happened using the new version.
>
>The files are attached and I sincerely appreciate your kind help and time!
>
>Very best regards,
>
>Jue
>
>Message: 3
>Date: Wed, 23 Apr 2008 22:27:57 -0400
>From: "Christopher Stiles" <CS145331 at albany.edu>
>Subject: RE: [gmx-users] x2top error in CNT simulation on Gromacs
>    3.3.3
>To: "'Discussion list for GROMACS users'" <gmx-users at gromacs.org>
>Message-ID:
>    <20080424022600.THIS1070.cdptpa-omta02.mail.rr.com at dreammachine>
>Content-Type: text/plain;    charset="us-ascii"
>
>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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