Dear Amber users,I'm working on proton transfer reaction using the evb model as implemented in amber14
I would like to simulate the proton transfer kinetic in different media such as protic or aprotic solvent
could some one help me with input file to adapt to my on work, or a protocol for performing MD with two states in the EVB model frameworkthank
Dr. Cyril Kenfack
Centre for Atomic Molecular Physics and Quantum Optics (CEPAMOQ) Faculty of Science - University of Douala P.O. Box 8580 Douala - CAMEROON Tel. actuel : 0023796031051 Fax: 237) 3343 46 08 Email: ckenf.yahoo.com
On Tuesday, July 26, 2016 8:24 PM, "Thakur, Abhishek" <axt651.miami.edu> wrote:
Thank you so much for your suggestion.
I will try to move as per your suggestions.
Thaking you all,
AT
________________________________
From: Marc van der Kamp <marcvanderkamp.gmail.com>
Sent: Monday, July 25, 2016 8:55:05 PM
To: AMBER Mailing List
Subject: Re: [AMBER] average pdb distorted
Never try to do (any type of) simulations with an average structure (see
also the post Hai linked).
Remember that an average structure is exactly that - coordinates averaged
over a trajectory. It is thus not a physically realistic structure!
What you more likely want is a representative structure, that you can get
through clustering.
And if you want to go directly from MM to QM/MM simulation (without
re-doing minimisation, heating etc.), you will need velocities as well...
Hope this helps,
Marc
On 25 July 2016 at 20:33, Thakur, Abhishek <axt651.miami.edu> wrote:
> I am planning to go for QM//MM calculations with the average structure
> generated.
>
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Monday, July 25, 2016 8:28:34 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] average pdb distorted
>
> Hi
>
> What's your aim of doing average?
> You can see a post about that here:
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.ambermd.org_201606_0394.html&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=ewguLVKTRZXe1xCgMNOT28TEFUA3NeASjSFGuQYM0e4&s=dTkhuLZVWqb1B1rr6gaVxJBseFY-ebqwQ7yVtX8XEuY&e=
>
> Hai
>
> On Mon, Jul 25, 2016 at 3:20 PM, Thakur, Abhishek <axt651.miami.edu>
> wrote:
>
> > Hi everyone,
> >
> > I am trying to make average pdb but every time my ligand get distorted.
> >
> > kindly help me out where I am doing mistake.
> >
> > Here is my scrip
> >
> >
> > trajin /WT_NH1_aMD_0_300ns.crd.gz
> > strip :WAT
> > strip :Na+
> > rms first mass @C,CA,N
> > average PRMT7_WT_NH1_aMD_avg_pdb.pdb pdb :1-344
> >
> >
> > Thanking you,
> >
> > AT
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Received on Sat Jul 30 2016 - 12:30:02 PDT
