AMBER Archive (2008)

Subject: Re: AMBER: MM_PBSA snapshot statistic calc problem

From: Vasu Chandrasekaran (
Date: Mon Sep 29 2008 - 14:08:15 CDT

If the snapshot_statistics.out file is not generated automatically, you can
manually generate the statistics output from your mmpbsa calculations using
the executable (a perl script) found in the mm_pbsa
directory (I think it will be under amber/src/).

Use the snapshot_statistics dot in as the input file, assign an output file
and if you have the snapshots of com, rec and lig from three different
trajectories, set calc_delta = 2. If you had extracted the snapshots from
the same trajectory, set calc_delta = 1. For both cases, you can set
calc_decomp to 0.

Hope that helps.


2008/9/27 haixiao jin <>

> dear Hannes,
> I have the same problem.
> have you solved it ?
> or any other amber users can give us some suggestion to solve this problem
> ?
> thank you!
> On Tue, Aug 5, 2008 at 8:45 PM, Hannes Wallnoefer <
>> wrote:
>> Hi amber-users,
>> I have a problem with the MM_PBSA tool in amber. To be sure that it is not
>> related to my system i downloaded the snapshots and the input files of the
>> tutorial A3: MM_PBSA.
>> When i perform the MM_PBSA calculation everything seems to be fine, but in
>> the
>> end the error: No data for 0+0 PB ELRAELE 0 appears and there is no
>> snapshots_statistics.out file. In the log-file the
>> mesage: 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
>> is found for every snapshot. I attached the log-file and the out-files
>> with all
>> of the calculated values.
>> Can anybody assist me with this problem?
>> Greetings
>> Hannes

Vasu Chandrasekaran
UNC-Chapel Hill
Ph: 706-296-7894 (Cell)

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to