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
Vince
PS: Its a modified peptide and I have only NOEs and hydrogen bond
restraints.
On 5 November 2015 at 20:49, David A Case <david.case.rutgers.edu> wrote:
> On Thu, Nov 05, 2015, V. Kumar wrote:
> >
> > I am trying to minimize my peptide in tip3pbox as demonstrated in this
> link
> > http://ambermd.org/doc6/html/AMBER-sh-4.2.html
>
> 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 instructions...you'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
