AMBER Archive (2007)

Subject: AMBER: Pribelm with Minimization & MD

From: saccenti_at_cerm.unifi.it
Date: Sun Sep 23 2007 - 13:27:20 CDT

Following CS advice, I changed nbt from 0 to 1 but I'm still having problem
More in details I'm trying to minimize a system in water and then using
this for PBSA calculations:

I attached all scripts I'm using

I'm doing the following:

- with two separate Leaps I add ions (leap_1) and waterbox (leap_2)
(t_leap.run)

Then I try to run three different minimization

1 Minimize waterbox holding fixed the protein (min_wat.in)
2 Minimize protein holding fixed the Water (min_prot.in)
3 Minimize the whole system (min_system.in)

I run this trough the script min_system.com

My calculations stalled @ the beginning of the minimization 1, and I get
the following min_wat.out:

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
 getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read

| peek_ewald_inpcrd: Box info not found in inpcrd
|Largest sphere to fit in unit cell has radius = 0.000

In both Leap_1.log and Leap_2.log I'm also getting the following (scary to
me) WARNING/ERROR

ERROR: The unperturbed charge of the unit: -1.698000 is not integral.
WARNING: The unperturbed charge of the unit: -1.698000 is not zero.

Many thanks for help
Edo 

-- 
Dr Edoardo Saccenti
CERM Magnetic Resonance Center
University of Florence
Fiorgen Foundation
Via Luigi Sacconi n° 6
50019 Sesto Fiorentino
(FI) Italy
Tel: +39 055 4574281
  • application/octet-stream attachment: leap_1_IN
  • application/octet-stream attachment: leap_2_IN
  • application/octet-stream attachment: tleap_run

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