[gmx-users] Hi ..

[Navratna Vajpai]

Dear Prof. David
Thanks for the suggestion. I just had a look for the various force  
field options. before starting my simulation I have a little queries..
1) Can I not use the same GROMOS force field g43b1 and then add HA  
afterwards by any other software or any other program in your package?
2)Can I use ffoplsaa (all atom force field) for the vacuum  
simulation? or should I use ffencadv for the simulation?
3) What does scaled-down vacuum charges mean? Is it different from  
the normal vacuum force field?
Many thanks and regards
Nav
  On Aug 17, 2006, at 9:11 AM, David van der Spoel wrote:

> Navratna Vajpai wrote:
>> Dear Mark
>> Hello.
>> The force field I used is g43b1 from GROMOS96. I checked the  
>> g43b1.atp file and fond that the HC is defined there which  
>> corresponds to Hydrogen attached to the Carbon. But somehow in the  
>> pdb outcome this is not there. the output pdb file contains only H  
>> atoms corresponding to HN. Now I exactly don't know which type of  
>> atoms are defined there. Kindly let me know what should I do to  
>> bring HA into the scene.
> use an all atom force field.
>
>> Best regards
>> Nav
>> On Aug 17, 2006, at 5:46 AM, Mark Abraham wrote:
>>> Navratna Vajpai wrote:
>>>> Dear All I have been able to carry on with the MD run of my  
>>>> peptides. But when I converted the traj into the pdb file I  
>>>> realized that there are no HA atoms in the pdb. I checked the  
>>>> rtp file and found that even those atoms are not defined there.  
>>>> So can anyone tell me how to get the HA (after or before the MD  
>>>> run) as i need them explicitly . I was trying to look for the  
>>>> options available in the trjconv but could not find.
>>>> Thanks and regards
>>>
>>> Does your force field include explicit non-polar hydrogen atoms?  
>>> Or does it use united atoms?
>>>
>>> Mark
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org <mailto: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 <mailto:gmx- 
>>> users-request at gromacs.org>.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> *******************************************
>> Navratna Vajpai
>> Ph. D student in Prof. Grzesiek's laboratory
>> Department of Structural Biology
>> Biozentrum, University of Basel
>> Klingelbergstrasse 70,
>> CH-4056
>> Basel, Switzerland.
>> Phone- +41 61 267 2080(O)
>>        +41 78 744 0810(M)
>> navratna.vajpai at unibas.ch <mailto:navratna.vajpai at unibas.ch>
>> --------------------------------------------------------------------- 
>> ---
>> _______________________________________________
>> 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

*******************************************
Navratna Vajpai
Ph. D student in Prof. Grzesiek's laboratory
Department of Structural Biology
Biozentrum, University of Basel
Klingelbergstrasse 70,
CH-4056
Basel, Switzerland.
Phone- +41 61 267 2080(O)
	       +41 78 744 0810(M)

navratna.vajpai at unibas.ch



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060817/222fbc41/attachment.html>