AMBER Archive (2009)

Subject: Re: [AMBER] mm_pbsa problem

From: Giorgos Lamprinidis (lamprinidis_at_pharm.uoa.gr)
Date: Wed Apr 01 2009 - 02:36:53 CDT

Ray and Dac thanks for you advices.
I rerun the job and it seems ok now. There were two problems. One with the
compilation and an other with my molecules.

Thanks guys

----- Original Message -----
From: "Ray Luo" <rayhuangluo_at_gmail.com>
To: "'AMBER Mailing List'" <amber_at_ambermd.org>
Sent: Monday, March 30, 2009 8:27 PM
Subject: RE: [AMBER] mm_pbsa problem

George,

Can you pass the tests in the updated mmpsa directories after the bugfix?
There is a makefile for all the tests under Example.

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 Giorgos Lamprinidis
Sent: Monday, March 30, 2009 7:00 AM
To: AMBER Mailing List
Subject: Re: [AMBER] mm_pbsa problem

dac,

Thanks for your advice.
I was not sure if i really did applied patch 17 so i recompiled ambertools
and amber 10 using bufix.all . The same error comes again.....

Dr George Lamprinidis
----- Original Message -----
From: "case" <case_at_biomaps.rutgers.edu>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Monday, March 30, 2009 3:48 PM
Subject: Re: [AMBER] mm_pbsa problem

> On Mon, Mar 30, 2009, Giorgos Lamprinidis wrote:
>>
>> I hgave amber v10.
>> I am trying to run a MMPBSA job using as a patern the A3 Advanced
>> Tutorial. At the last step, when i want to create the
>> snapshot_statistics.out file i get the next warning message for all the
>> snapshots:
>> =>> Reading files
>> Reading snapshot_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
>> ....................................
>> and then the calculation stops on,
>> =>> Calc delta from raw data
>>
>> i thougt there was something wrong with my codes so i downloaded all the
>> out files from the tutorial and i tried to run the tutorial's last
>> calculations, to reproduce the snapshot_statistics.out from the Tutorial.

>> I got the same messages.....
>> I searched alot on the amber mailing list. I saw many threads about that
>> issues but i didn't find any reply with solution.
>>
>
> Have you applied bugfix.17?
>
> ...dac
>
>
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