AMBER Archive (2004)

Subject: AMBER: nmode & mm-pbsa

From: Shekter, Lee (Lee_Shekter_at_brown.edu)
Date: Thu Dec 02 2004 - 20:50:45 CST

Hello -
I am running the mm-pbsa module of AMBER8 on Solaris. If I don't set nmode to run (NM 0) then everything works fine: the program runs and finishes successfully. But when I select NMODE to be on (NM 1), NMODE fails with the following error:
 
Root-mean-square gradient of input coords is 3.403315169369272
 This is greater than the requested maximum: 1.0
 
This error, as far as previous posts go, suggested that nmode was not run with the same dielectric constant as sander, even though they were supposed to be the same as evidenced by the input file to mm_pbsa.pl, part of which is shown below.
                             
####################################################################
@PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2.0
LINIT 500
PRBRAD 1.6
#
RADIOPT 1
#
FOCUS 0
PERFIL 80.0
CHARGE ./my_amber94_delphi.crg
SIZE ./my_parse_delphi.siz
#
SURFTEN 0.005
SURFOFF 0.0
#
############################
@MM
DIELC 1.0 <---
#############################
@GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
############################
@MS
PROBE 0.0
###########################
@NM
DIELC 1.0 <---
MAXCYC 1000
DRMS 0.1
 
But the input file for nmode says otherwise:
 
File generated by mm_pbsa.pl
 &data
  ntx = 0,
  ntrun = 1, nvect = 0,
  drms = 1,
  dielc = 4.0, <=== idiel = 0,
  scnb = 2.0, scee = 1.2
 &end
 
If I change dielc = 4.0 to dielc = 1.0 in the nmode input file and run nmode directly it runs fine. How did the dielectric constant change to 4.0?
Thanks in advance,
 
Lee Shekter
Assistant Professor (Adjunct) Medical Science
Brown University
Divison of Biology and Medicine
Box G
Providence, RI 02912-9107
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