AMBER Archive (2007)

Subject: Re: AMBER: mm-pbsa error with nm = 1

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Tue May 01 2007 - 18:58:17 CDT

In addition to other useful comments, you may also want to add the following parameters in your input.

@MM
DIELEC 1
@NM
DIELEC 4
MAXCYC 100000
DRMS 0.0001

you may also want to remove
@PROGRAMS
head in your input since you do not seem to need it.

Hope this helps,

jenk

Hayden Eastwood <s0237717_at_sms.ed.ac.uk> wrote: Dear Amber users

I'm running mm-pbsa on a small protein complex. When I run mm-pbsa with nm
set to 0, everything works fine. However, when I set nm = 1 so that I can
compute the entropy of the system the program crashes out whilst performing
the sanity check and gives me the following error message:

Param DIELC does not exist

My input file is as follows:

@GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./HBD1_2SU.parm
RECPT ./HBD1.parm
LIGPT ./2SU.parm
GC 0
AS 0
DC 0
MM 1
GB 1
PB 1
MS 1
NM 1

@PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
SURFTEN 0.0072
SURFOFF 0.00
@MM

@GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
@MS
PROBE 0.0
@PROGRAMS

Any ideas as to how to get round the crash out?

Many thanks in advance

Hayden Eastwood

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