navratna.vajpai at unibas.ch
Thu Sep 14 15:50:05 CEST 2006
Sorry for not so explicitly explaining the things.. Here it goes
I have a nona peptide and I ran a MD of 20ns using OPLS-AA force field.
when I used the OPLS-AA the phi angles came out to be -ve for three
of the amino acids. which is stericaly not allowed. But when I ran it
using GROMOS I found all the phi-psi combinations with a negative phi
value distribution. But now I am lost as you have said it works only
for GROMOS like force field. Why?
and if that so I have got -ve phi distribution for the other phi-psi
My other question remained unanswered even now. Is there any way
really to judge which force field is to be chosen for particular type
On Sep 14, 2006, at 3:36 PM, David van der Spoel wrote:
> Navratna Vajpai wrote:
>> Hi all.. I wrote this mail yesterday. But could not receive any
>> reply till now. So if someone can suggest something about it. That
>> would be nice. Best regards
>> Begin forwarded message:
>>> *From: *Navratna Vajpai <navratna.vajpai at unibas.ch
>>> <mailto:navratna.vajpai at unibas.ch>>
>>> *Date: *September 13, 2006 10:32:21 AM GMT+02:00
>>> *To: *Discussion list for GROMACS users <gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>>
>>> *Subject: **[gmx-users] Hi...*
>>> *Reply-To: *Discussion list for GROMACS users <gmx-
>>> users at gromacs.org <mailto:gmx-users at gromacs.org>>
>>> Dear All
>>> Hi.. This is in regard to your previously replied mail regarding
>>> the use of GROMOS96 or OPLS-AA or AMBER force field.
>>> As you said it depends upon the users taste which one to use.
>>> This means that the three on a broad manner should give
>>> convergence of the analyzed data set. Infact from my simulation
>>> runs using oplss-aa and gromos96, I didn't found that. I tried
>>> using the GROMOS96 and opls-aa force field on my small peptides
>>> for a period of 20ns and found that with opls-aa even the phi-psi
>>> combination of the individual amino acids were incorrect.
>>> Actually this always puzzled me to make a choice for the Force
>>> field. The rest of the script was unchanged for the two runs.
>>> Could you please comment on the above results? Is there any way
>>> really to judge which force field is to be chosen for particular
>>> type of analysis?
>>> Best regards
> what do you mean with incorrect? your question is quite vague.
> the g_rama program works only for GROMOS like force fields
> unfortunately but that doesn't mean the phi/psi are wrong. What
> would be the "correct" result anyway? Maybe your peptide unfolds.
> 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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Ph. D student in Prof. Grzesiek's laboratory
Department of Structural Biology
Biozentrum, University of Basel
Phone- +41 61 267 2080(O)
+41 78 744 0810(M)
navratna.vajpai at unibas.ch
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