[gmx-users] Hi ..

[David van der Spoel]

Navratna Vajpai wrote:
> 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?
No, that would be meaningless.

> 2)Can I use ffoplsaa (all atom force field) for the vacuum simulation? 
> or should I use ffencadv for the simulation?

ffoplsaa is fine as long as you look into the protonation state of the 
side chains which is non-trivial.

> 3) What does scaled-down vacuum charges mean? Is it different from the 
> normal vacuum force field?

neutralized side chains usually.

> Many thanks and regards

Please read the following papers:

@Article{Jorgensen96a,
   author = 	 {W. L. Jorgensen and D. S. Maxwell and J. {Tirado-Rives}},
   title = 	 {Development and testing of the {OPLS} all-atom force field 
on conformational energetics and properties of organic liquids},
   journal = 	 {J. Am. Chem. Soc.},
   year = 	 1996,
   volume =	 118,
   pages =	 {11225-11236}
}

@Article{Jorgensen2005a,
   author = 	 {William L. Jorgensen and Julian Tirado-Rives},
   title = 	 {Potential energy functions for atomic-level simulations of 
water and organic and biomolecular systems},
   journal = 	 {Proc. Natl. Acad. Sci. USA},
   year = 	 2005,
   volume =	 102,
   pages =	 {6665-6670 }
}

@Article{Christen2005a,
   author = 	 {Markus Christen and Philippe H. H{\"u}nenberger and Dirk 
Bakowies and Riccardo Baron and Roland B{\"u}rgi and Daan P. Geerke and 
Tim N. Heinz and Mika A. Kastenholz and Vincent Kr{\"a}utler and Chris 
Oostenbrink and Christine Peter and Daniel Trzesniak and Wilfred F. van 
Gunsteren},
   title = 	 {The GROMOS software for biomolecular simulation: GROMOS05},
   journal = 	 {J. Comp. Chem.},
   year = 	 2005,
   volume =	 26,
   pages =	 {1719-1751}
}




> 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
>>>> _______________________________________________
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>>> *******************************************
>>> 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>
>>> ------------------------------------------------------------------------
>>> _______________________________________________
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>>
>>
>> -- 
>> 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 <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org   
>> http://folding.bmc.uu.se
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> 
> *******************************************
> 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>
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
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
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