[gmx-users] parameters for protonated nitrogen

Samuel Coulbourn Flores 花山 scflores at stanford.edu
Tue Aug 5 07:20:54 CEST 2008

Hi Guys,

I have a molecule with a nitrogen bonded to three carbons and one  
proton.  Can anyone tell me what parameters to use?  I have looked  
through the amber parameter file and can't find suitable parameters.   
I'm not sure if it is probable, but if the N1 of cytidine were  
protonated, it would be similar to my situation.

Many thanks,


On Sep 26, 2007, at 3:27 AM, janne.hirvi at joensuu.fi wrote:

> Thanks for your help Alan, Yang, and Belquis!
> Now I managed to get trajectory in which a droplet stays in the  
> middle of the simulation box while a surface moves below the  
> droplet. First I used trjconv to remove periodicity (-pbc nojump)  
> and then performed translational fit for the droplet (-fit  
> translational) and finally transferred all the translating surface  
> atoms back to the simulation box (-pbc -inbox).
> However, there is still a problem with fitting procedure which is  
> performed in three dimension and hence the surface translates  
> upwards during the video. It should be quite easy to modify trjconv  
> so that the fitting is performed only for the xy coordinates (not  
> for the z coordinate perpendicular to the surface) but with my  
> programming skills I wasn't able to do that (actually I wasnt able  
> to find the correct lines). So I would like to know if someone has  
> made a such modification to trjconv (trjconv_d) or could help me to  
> do it?
> Thanks,
> Janne
>> Hello Janne,
>> this is what I usually do when my molecules cross the box or dance  
>> all
>> around and it works for me:
>> I first do this with the "original" unmodified or fitted xtc or trr  
>> file:
>> trjconv -f  -o  -pbc nojump
>> then i take the modified trr or xtc and do a fit:
>> trjconv -f -s -fit rot+trans
>> Belquis
>>> Hello gmx-users!
>>> I am trying to make a simulation video in which a water droplet is
>>> rolling or sliding on a surface. Due to a periodic boundary  
>>> conditions
>>> a droplet is not whole all the time but it disappears from the right
>>> and appears from the left in cycles.
>>> I think that I could create more visual video by removing the  
>>> lateral
>>> motion of the center of mass of a droplet so that the droplet would
>>> stay whole
>>> in the middle of simulation window and the surface would translate
>>> below the droplet. I am not exactly sure how realistic this kind of
>>> video would be and would like to know if someone has better ideas?
>>> If there are no better ideas I would need advices to be able to  
>>> create
>>> a such trajectory or video. Right now I am struggling with trjconv
>>> which might be suitable for this purpose. However, if I use the
>>> droplet as a group for translational fit (-fit translation) I get
>>> trajectory in which the whole system wanders strangly (laterally  
>>> (the
>>> surface moves first to the left and then back to the right) and also
>>> in perpendicular to the surface due to the lowering of the height of
>>> the center of mass of the droplet during the simulation) and the
>>> droplet wont stay whole in the middle of the box. Any ideas what I  
>>> am
>>> doing wrong or how I would be able to get rid of even this lateral
>>> wandering so that I could at least see how realistic this  
>>> procedure is?
>>> Thanks for your time and help in advance,
>>> Janne
>>> ------------------------------------------------------------------------------
>>> Janne Hirvi, MSc(Physical Chemistry), Researcher
>>> University of Joensuu, Department of Chemistry, P.O.Box 111 80101  
>>> Joensuu,
>>> FI
>>> Tel: +358 13 2514544 & +358 50 3474223
>>> E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
>>> ------------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> 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

Samuel Coulbourn Flores, PhD
Altman Lab
Department of BioEngineering
Stanford University
samuel.flores at aya.yale.edu


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080804/9bae5fbe/attachment.html>

More information about the gromacs.org_gmx-users mailing list