AMBER: mm_pbsa: problems with dielec constant when using

From: Magne Olufsen <Magne.Olufsen.chem.uit.no>
Date: Thu, 15 Sep 2005 13:02:35 +0200

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.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Sep 15 2005 - 12:53:00 PDT
Custom Search