AMBER Archive (2009)

Subject: Re: [AMBER] MM - PBSA problem

From: musa özboyacı (musaozboyaci_at_gmail.com)
Date: Thu Jan 22 2009 - 13:52:10 CST

Dear Ray,
I am using Amber 10. I created the coordinates files without any problem.
So, I attach the energy input file. Thanks in advance!

Musa

2009/1/22 Ray Luo <rayhuangluo_at_gmail.com>

> Dear Musa,
>
> Could you be more specific on which distribution of Amber you are using?
> What's your input file?
>
> All the best,
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Associate Professor
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900 Email: rluo_at_uci.edu
> Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf
> Of musa özboyacı
> Sent: Thursday, January 22, 2009 9:07 AM
> To: AMBER_at_ambermd.org
> Subject: [AMBER] MM - PBSA problem
>
> Dear Amber users,
> I've trying to use mm-pbsa tool of AMBER, and everytime I use I get the
> same
> error. I tried every possible suggestions in the old mails. However I
> couldn't fix the problem. I would be very glad if you help me. Here is my
> output:
>
>
> =>> Values of global variables
> TEMP = 300
> R = 8.314
> gammaP = 0.00542
> betaP = 0.92
> gammaG = 0.0072
> betaG = 0
> =>> Reading input
> =>> Reordering files
> Final order:
> 1. qq2_com.all.out: -
> 2. qq2_rec.all.out: -
> 3. qq2_lig.all.out: -
> =>> Reading files
> Reading qq2_com.all.out
> WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
> WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
> WARNING: Missing EPB for PB in 0 -> Taken from -1
> WARNING: Missing PBNONPOL for PB in 1 -> Taken from 0
> WARNING: Missing ELRAELE for PB in 1 -> Taken from 0
> WARNING: Missing EPB for PB in 1 -> Taken from 0
> WARNING: Missing PBNONPOL for PB in 2 -> Taken from 1
> ........
> =>> Treat special parameters
> =>> Calc missing parameters
> Processing MM GAS
> Doing 1 MM ELE
> No values for MM_ELE existing -> Skipping
> Processing MM INT
> ........
> =>> Calc delta from raw data
> No data for 0+0 PB ELRAELE 0
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