Re: [AMBER] internal geometry restraint

From: Jio M <>
Date: Mon, 2 Dec 2013 09:50:42 -0800 (PST)

Dear David

Thanks for reply. Sorry I forgot to ask, what are units for contraining constant (fcons): is it kcal/mol/A**2

kind regards

On Monday, December 2, 2013 1:07 PM, David A Case <> wrote:
On Thu, Nov 28, 2013, Jio M wrote:
> 3) I am not sure about ifit flag (default ifit=0). Lets say if I use
> starting simulation structure (rst file) different from mapfile then I
> should use ifit =1? But in my case del.pdb which is obtained from prmtop
> and rst itself so ifit =0 seems ok.

Since the starting coordinates already match the starting map, there is no
need to do any initial fitting of the map to the coordinates.  Certainly, you
should experiment with both options to see if there are differences.

> 5) grid again kept default; honestly not sure about this grid fitting,
> can default values be considered as 'ideal value'? In order to keep
> internal geometry strictly according to mapfit (del.pdb) which one should be
> changed: fcons or grid? (I tried increasing fcons to 10 and I get vlimit
> error; keeping fcons=1 more or less works fine anyhow)

A small fcons value is usually required; another key parameter is the
resolution of the (pseudo-)map.  This will help determine how "rigid" the
domains are -- a lower resolution (numerically higher number) will allow
somewhat more movement within each domain.

...good luck...dac

AMBER mailing list
AMBER mailing list
Received on Mon Dec 02 2013 - 10:00:03 PST
Custom Search