Re: AMBER: GPCR membrane simulation, setting surface tension

From: Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de>
Date: Tue, 12 Aug 2008 10:45:08 +0200

Dear Fiona,

There is no option in Amber to add surface tension to your system (at
least as far as I am aware of).As far as I know the article you cite
here, only talks about POPC and not DPPC. Maybe you want to check the
articles below as well. Even with the gaff force field, I would suggest
you to use NAMD for your membrane simulations, as NAMD has more options
regarding pressure control (including the surface tension option) and it
accepts amber topologies as input. From the tests I have performed so
far, doing NPT in AMBER with ntp=2 leads to more unrealistic membrane
properties than doing NPT in NAMD with the Langevin piston method to
control the pressure (if somebody has more experience here please carve
in). Adding surface tension or not to the simulation is matter of
debate. Its up to you to decide whether you really want to add it or
not. It depends at which membrane properties you're looking at ... You
should do some reading on the topic before deciding if you really want
to add surface tension.

If you decide to use NAMD for the simulations please read very carefully
the paragraph about using the AMBER force fields in NAMD
(http://www.ks.uiuc.edu/Research/namd/2.6/ug/node15.html).

As a general remark, using gaff with membranes should still be regarded
as experimental .. I am not saying here you shouldn't use it as I am
using it myself but I would suggest lots of reading and first do a
simulation only with the membrane to see how it behaves ...

Best wishes
vlad

Siu SW, Vcha R, Jungwirth P, Bo"ckmann RA.
<http://www.ncbi.nlm.nih.gov/pubmed/18376978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum>

Biomolecular simulations of membranes: physical properties from
different force fields.
J Chem Phys. 2008 Mar 28;128(12):125103.
PMID: 18376978 [PubMed - indexed for MEDLINE]

Rosso L, Gould IR.
<http://www.ncbi.nlm.nih.gov/pubmed/17910006?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum>

Structure and dynamics of phospholipid bilayers using recently developed
general all-atom force fields.
J Comput Chem. 2008 Jan 15;29(1):24-37.
PMID: 17910006 [PubMed - indexed for MEDLINE]




Fiona McRobb wrote:
> Dear Amber Users,
> I am simulating a GPCR in a DPPC membrane, using AMBER 9 and I am
> using the recent journal article by Jjrt, B., /et al/. (/J. Chem.
> Inf. Model. /*2008,* 48(6), 1199-1210.) as a guide for the simulation
> conditions.
> Following minimisation, I have heated the system to 310K using NVT
> ensemble. I will then be running equilibration dynamics and I am
> trying to determine the best type of ensemble to use, either NPT or
> NPT. Hence, I will be running simulations with both types of
> ensembles to determine which one I should use. Which brings me to my
> question - is it possible to set the surface tension in AMBER and if
> it is possible, which settings do I need to employ to achieve this?
> Being a new user of AMBER,I have looked through the manual extensively
> for the method to set the surface tension, but I have been unable to
> find the setting I am looking for.
> Any help or suggestions would be greatly appreciated,
> Regards,
> Fiona
> Fiona M. McRobb B.Med.Chem.(Hons)
> PhD Candidate
> Phone:+61 3 99039165
> Email: Fiona.McRobb.vcp.monash.edu.au
> <mailto:Fiona.McRobb.vcp.monash.edu.au>
> Medicinal Chemistry and Drug Action
> Monash Institute of Pharmaceutical Sciences
> Monash University (Parkville Campus)
> 381 Royal Parade, Parkville
> Victoria 3052, Australia

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
----------------------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo.scripps.edu
Received on Wed Aug 13 2008 - 06:07:37 PDT
Custom Search