AMBER: Pribelm with Minimization & MD

From: <>
Date: Sun, 23 Sep 2007 20:27:20 +0200 (CEST)

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)

Then I try to run three different minimization

1 Minimize waterbox holding fixed the protein (
2 Minimize protein holding fixed the Water (
3 Minimize the whole system (

I run this trough the script

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


| 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

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

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

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Received on Mon Sep 24 2007 - 17:45:08 PDT
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