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: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> 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
