Re: [AMBER] NMR restraints + minimization+Could not find cntrl namelist

From: V. Kumar <>
Date: Thu, 5 Nov 2015 21:57:17 +0100

Dear David

Yes, that post from 2000. Yet for my present problem that tutorial is
highly suited. I have annealed my peptide in GB model with igb=5, now from
this best structure (GB) I want to refine it in explicit solvent with
restraints ON i.e restrained dynamics(rMD) for 20 ps with loop.

I'm currently using amber12. Could I request you "input files" or link to
find for input files with restraints on for explicit solvent.

In fact, input file didn't work when I adjusted the space similar to
working inputs of amber 12.

thanks in advance..

Best wishes

PS: Its a modified peptide and I have only NOEs and hydrogen bond

On 5 November 2015 at 20:49, David A Case <> wrote:

> On Thu, Nov 05, 2015, V. Kumar wrote:
> >
> > I am trying to minimize my peptide in tip3pbox as demonstrated in this
> link
> >
> Oooohhh, this is evil. Amber version 6 was released in the last century
> (not
> to mention the last millenium!) I guess it is some tribute to our work on
> backwards compatibility that relatively little has changed for more or less
> standard inputs.
> It's not clear what version of sander you are using. Current versions
> have no
> trouble with multiple lines in the title section.
> (I've removed these old'll have to use the WayBack
> machine
> if you really need them....)
> ....dac
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Received on Thu Nov 05 2015 - 13:00:03 PST
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