[gmx-users] cgnr charge classifying

David van der Spoel spoel at xray.bmc.uu.se
Sun Jun 4 13:18:19 CEST 2006


davood ajloo wrote:
> I want to construct the trp file for a nanotube, I used prodrg but it 
> could not calculate for non flat sp2 carbon(nanotube) .  I used X2top to 
> creating the top file from pdb (from Hyperchm), It only gave me the 
> connetction, no bond and angles and others parameters. I got them from 
> literature and put them in the top file and calculated the charge from 
> quantum mechanics program. In topology file the charges were oredred on 
> the cgnr group. It is on the basis of the group which sum of their 
> charges are zero. But I dont know how I order charge for nanotube. 
> finally how I can the topology file for carbon nanotube
> with best regards
there's quite a few people simulating CNTs with GROMACS. Ask for a 
topology from someone, or search the mailing list.
x2top should be able to give you a .top file including bonds and angles 
etc. but not charges.

> Ajloo
> 
> */David van der Spoel <spoel at xray.bmc.uu.se>/* wrote:
> 
>     davood ajloo wrote:
>      > Dear gmx-users
>      > I want to classifying the charge on the basis of cgnr charge
>     type. How I
>      > do it?
>     please explain better what you want to do.
> 
>      > Thanks a lot of
>      > Ajloo
>      >
>      > __________________________________________________
>      > Do You Yahoo!?
>      > Tired of spam? Yahoo! Mail has the best spam protection around
>      > http://mail.yahoo.com
>      >
>      >
>      >
>     ------------------------------------------------------------------------
>      >
>      > _______________________________________________
>      > 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.
>      > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
>     -- 
>     David.
>     ________________________________________________________________________
>     David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
>     ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>     _______________________________________________
>     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.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



More information about the gromacs.org_gmx-users mailing list