AMBER Archive (2008)

Subject: Re: AMBER: nmode units

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Thu Sep 04 2008 - 10:22:41 CDT

My output is like that below. It is already T*S. So it is ever kcal/mol
(what I expect), or cal/mol. The only thing here I want to be absolutely
sure what exactly units are in mm_pbsa outputs i will use. Because in
the output or in manual those are not marked.

# COMPLEX RECEPTOR
LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= ======================= ====
TSTRA 16.83 0.00 16.81 0.00
13.49 0.00
TSROT 17.29 0.01 17.29 0.01
11.65 0.04
TSVIB 2450.02 13.20 2393.15 5.17
54.80 0.53
TSTOT 2484.15 13.21 2427.25 5.17
79.94 0.57

# DELTA
# -----------------------
# MEAN STD
# =======================
TSTRA -13.46 0.00
TSROT -11.65 0.04
TSVIB 2.07 12.39
TSTOT -23.04 12.41

David A. Case wrote:
> On Thu, Sep 04, 2008, Arturas Ziemys wrote:
>
>> If I run entropy calculations, nmode is invoked through mm_ppbs scripts.
>> My statistics output contains no info on vibrations. But it contains
>> entropy estimate. So I am wandering what are those units, as output
>> contains just values.
>>
>
> Compare the numbers in the nmode output itself to what mm_pbsa collects.
> Nmode computes entropies in entropy units (cal/mol-K), and its outputs
> are clearly labelled.
>
> ....dac
>
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-- 

Arturas Ziemys, PhD
  School of Health Information Sciences
  University of Texas Health Science Center at Houston
  7000 Fannin, Suit 880
  Houston, TX 77030
  Phone: (713) 500-3975
  Fax:   (713) 500-3929  

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