Re: [AMBER] Fixed Minimization

From: emanuele falbo <>
Date: Fri, 6 Dec 2019 15:05:14 +0000

Hi David,

thanks for the heads-up. Yes, the -ref flag is the same as the -c one.
However, I have used the "ibelly" flag and now it works like a charm.
I am going to post my input file for anyone else who'd have the same issue.

  bellymask='!(:1)', # Minimize everything apart from residue 1

Also, I just want to point out that only in this case I experienced that a
such high positional restraint, like 5000 kcal/mol (ntr=1)
did not work, whereas it is fine for the rest of the simulations I have
been doing.
I do not have a proper answer to that, but I suspect that there must be
something to do
with the different way of how belly deals with restrains ? Thanks anyway.


Il giorno ven 6 dic 2019 alle ore 13:26 David A Case <>
ha scritto:

> On Thu, Dec 05, 2019, emanuele falbo wrote:
> >
> >I am trying to run a Minimization with one residue coordinates fixed.
> >However, no matter how large the restraint constant it is, the residue
> >keeps being minimised.
> How far does it move? How big is the restraint energy? Is the -ref
> file the same as the -c file? (That is, is the restraint energy zero on
> step 1?)
> You could also use the belly option to allow only residues greater than
> 1 to move.
> ....dac
> _______________________________________________
> AMBER mailing list

*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
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Received on Fri Dec 06 2019 - 07:30:01 PST
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