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)
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________________________________________________________________________
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
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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)
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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