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 Mon Jul 25 2016 - 13:00:03 PDT
