[gmx-users] Hi...

[Mu Yuguang (Dr)]

OPLS-aa force field is good for beta structure, it is not so good for
alpha helix study.

Amber99f force field is good for alpha helix , but not good for beta
structure

 

Best regards

Yuguang

 

Dr. Yuguang Mu

Assistant Professor

School of Biological Sciences

Nanyang Technological University

60 Nanyang Drive  Singapore 637551 Tel: +65-63162885 Fax: +65-67913856

http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php

 

________________________________

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Navratna Vajpai
Sent: Thursday, September 14, 2006 9:50 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Hi...

 

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
plots. 

My other question remained unanswered even now. Is there any way really
to judge which force field is to be chosen for particular type of
analysis?

Best regards 

Thanks

 

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

	Nav

	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

		Nav

		 

 

 

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.

________________________________________________________________________

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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*******************************************

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

 





 

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