[gmx-users] on x2top, Need for help!

[David van der Spoel]

On Mon, 2003-12-15 at 02:36, 徐志平 wrote:
> Dear all:
>      I am trying to run MD simulations on carbon nanotube, so I generate
> my coordinate file as:

Is the box described in your pdb file as a proper
CRYST
record? Check the output on screen for stuff related to the the program
generating a box.

Otherwise try the new gromacs 3.2.0 beta, I did make some small changes
to x2top, and I vaguely recall that it has worked on a nanotube.

> 
> CNT.pdb
> --------------------------------------------------------
> Carbon Nanotube
> 600
>     1CNT  CB  1    0.274  0.199  -1.167  
> .......
>     40 23.15 40
> --------------------------------------------------------
>      then I run 
>           >x2top -f CNT.pdb -o CNT.top -r CNT.rtp
>           with a selection on 0: Gromacs forcefield.
>      but it reports an error as "no forcefield type for atom CB(1) with
> 2 bonds", so I check the previous posts, someone suggested to have a
> modification on ffgmx.n2t.
>      so I add some lines below  "CB  CB  3  CB  CB  CB", but  I am not
> sure because I am not familiar with those files.
> --------------------------------------------------------
> CB  CB  3  CB   CB      CB
> CB  CB  2  CB   CB
> --------------------------------------------------------
>        then it works well, furthmore I'd like to use periodic boudary
> condition, and run 
>           >export GMXFULLPBC=1
>           >x2top -f CNT.pdb -o CNT.top -r CNT.rtp -pbc
>           But it does not work, the atoms near one boundary are not
> bonded with those near the oppsite one, I do not know if x2top read PBC
> from the last line of *gro file.
>           Can anyone help me? Thanks a lot.
> 
> 
> Best Regards.
> 
> ZP
> 
> -----------------------------------------------
> 徐 志平 / Xu ZhiPing
> Ph.D Candidate
> Room: 3405, Phone: 86-10-627-83814
> Department of Mechanics,
> Qinghua University, Beijing, CHINA
> -----------------------------------------------
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++