AMBER Archive (2005)

Subject: AMBER: mm_pbsa: problems with dielec constant when using

From: Magne Olufsen (Magne.Olufsen_at_chem.uit.no)
Date: Thu Sep 15 2005 - 06:02:35 CDT

Dear AMBER develpers

I am currently using the mm_pbsa script to calculate the entropy with
nmode. The script works for different dielc values except dielc = 1, then
the job dies. Here is the masage I got when the program dies:
/opt/amber8/exe/nmode -O -i nmode_lig.in -o nmode_lig.1.out -c
sanmin_lig.1.restrt -p ./raf_wt.prmtop not running properly

In the nmode_lig.in file, which is generated by the mm_pbsa script, the
dielc is 4 even if it is set to 1 in the mm_pbsa.in file

I have tested the snapshots from the example files as well, and the same
happens with these coordinates. Is'nt it possible to use dielc=1 in the
mm_pbsa script or is it a bug in the program?

Greetings from Magne Olufsen, Ph.D. student from Norway.

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