Re: [AMBER] Production md

From: ariana karakutuk <>
Date: Tue, 14 Aug 2012 07:19:56 +0000

Thanks for replying. We've prepared the missing residues using the software COOT. During dynamics the protein behaves normally, but the solvent ions (3 Na+ ions) diffuse very far away from each other. First I've done minimization, there was no error. Here's the input file:
&cntrlimin=1, maxcyc=1000, ncyc=500,cut=999., rgbmax=999., igb=1, ntb=0,ntpr=100/
Then I've continued for the heating. There was no error. Here's the input file:
&cntrlimin=0, irest=0, ntx=1,nstlim=25000, dt=0.0005,ntc=2, ntf=2,ntt=1, tautp=1.0,tempi=0.0, temp0=300.0,ntpr=50, ntwx=50,ntb=0, igb=1,cut=999., rgbmax=999./Hold the protein fixed100.0RES 1 8 27 105ENDEND
After heating, I've started for equilibration, but the problem has occured.

> Date: Mon, 13 Aug 2012 08:35:01 -0400
> From:
> To:
> Subject: Re: [AMBER] Production md
> On Mon, Aug 13, 2012, ariana karakutuk wrote:
> > I'm new in AMBER. I'm trying to fold the missing sequences of a protein,
> > but in the result the molecules diffuse very far away from each
> > other. Here's my input file:
> Please describe your calculation in more detail. It looks like maybe(??)
> you have (experimental?) coordinates for residues 1-8 and 27-105, but not for
> residues 9-26. But you don't say how you prepared the initial coordinates,
> nor what the "molecules" are that diffuse far away from each other. It's hard
> to give any good advice without more idea of what you did.
> [Note: if you do have a big stretch of missing residues in a single
> polypeptide chain, Amber is not a very good program to estimate where the
> missing pieces are. In this case, you would probably want a homology modeling
> program of some sort.]
> ....dac
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Received on Tue Aug 14 2012 - 00:30:03 PDT
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