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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> > AMBER.ambermd.org
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=ewguLVKTRZXe1xCgMNOT28TEFUA3NeASjSFGuQYM0e4&s=3mrO_DAVfdLUq0MImcomHNmhc6O0tA11TOmKSGDB1so&e=
> >
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Received on Tue Jul 26 2016 - 01:00:02 PDT
