[gmx-users] amber-lipid

[ABEL Stephane 175950]

Hi, 

In my  opinion use Amber ff to simulate phospholipids is a bad idea. An alternative is to use GAFF with the good RESP charges. 

See these papers where several phospholipids are simulated with the GAFF ff.

(1) Siu, S. W. I.; Vácha, R.; Jungwirth, P.; Böckmann, R. A.; Shirley, S. W. I.; Robert, V.; Pavel, J.; Rainer, A. B. The Journal of chemical physics 2008, 128, 125103.
(2) Rosso, L.; Gould, I. R. J. Comput. Chem. 2008, 29, 24-37.

HTH

Stephane

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Message: 7
Date: Mon, 6 Feb 2012 14:04:21 +0200
From: ??????? ???????? <rayevsky85 at gmail.com>
Subject: [gmx-users] amber-lipid
To: gmx-users at gromacs.org
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Hi
Is it possible to use amber forcefield with lipid parameters like it
was done with gmx in "KALP-15 in DPPC" tutorial?
I have to use amber forcefield as it is neccessary for parametrization
of my ligand and its stecking interactions.

Thank you very much

--



Nemo me impune lacessit


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Message: 8
Date: Mon, 6 Feb 2012 17:39:54 +0530
From: Anushree Tripathi <anushritripathi at gmail.com>
Subject: Re: [gmx-users] problem with nvt equilibration
To: jalemkul at vt.edu, Discussion list for GROMACS users
        <gmx-users at gromacs.org>
Message-ID:
        <CAAx43BzE=yB3FK=2LcKTmUL9+tmpJ_hb6WqrX6iBmd60p8qqBQ at mail.gmail.com>
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Will you please send me the basic tutorial in which I can find how to use
-n option in " grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr" command.

On Mon, Feb 6, 2012 at 5:17 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Anushree Tripathi wrote:
>
>> where should I use -n option in the command (i.e., grompp -f nvt.mdp -c
>> em.gro -p topol.top -o nvt.tpr).Please tell me.
>>
>>
> I would suggest you refer to grompp -h and/or go through some basic
> tutorial material so that you can get a feel for command line options and
> how to apply them.
>
> -Justin
>
>  On Mon, Feb 6, 2012 at 4:58 PM, Mark Abraham <Mark.Abraham at anu.edu.au<mailto:
>> Mark.Abraham at anu.edu.**au <Mark.Abraham at anu.edu.au>>> wrote:
>>
>>    On 6/02/2012 8:28 PM, Anushree Tripathi wrote:
>>
>>        Inspite of having DPPC in index file,when I run the command (
>>        i.e., grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr ),I am
>>        getting the error:
>>
>>        Group DPPC not found in indexfile.
>>        Maybe you have non-default goups in your .mdp file, while not
>>        using the '-n' option of grompp.
>>        In that case use the '-n' option.
>>
>>        Now, what to do? Please guide me.
>>
>>
>>    You seem not to have used the -n option. You could try using it. :)
>>
>>    Mark
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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