AMBER Archive (2008)

Subject: RE: AMBER: How to transfer unformatted coordinates into formatted ones

From: Qi Yan (kid1412_at_uab.edu)
Date: Wed May 07 2008 - 21:55:18 CDT

Hi,

I have tried to do 0-step minimization in sander by selecting either
ntx=2 or ntx=4, but my input file still can not work. Did some people
use unformatted coordinate as inpcrd to do minimization before?

This is my input file:
 &cntrl
  ntx = 2,
  ntxo = 1,
  ntf = 1, ntb = 1,
  dielc = 2,
  cut = 99.0, nsnb = 99999,
  scnb = 2.0, scee = 1.2,
  imin = 1, maxcyc = 0,
  ncyc = 0, drms = 0.0001
 &end
 &ewald
  eedmeth= 5,
 &end

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of David A. Case
Sent: Wed 5/7/2008 8:14 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: How to transfer unformatted coordinates into
formatted ones
 
On Wed, May 07, 2008, Qi Yan wrote:
>
> Does anybody know how to transfer an unformatted coordinate file into
> formatted one?

You can do a 0-step minimization in sander (actually equivalent to a
1-step
minimization), and read in the unformatted file and write out a
formatted one.

Haven't tried this, but it should work...good luck...dac

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