Hi, all.
I'm trying to calculate pmf using gibbs, so
I made a simple model to understand the program.
$namelist read: read unexpected character
apparent state: unit 5 named umb.in
last format: list io
lately reading sequential formatted external IO
[1] Abort gibbs -O -i umb.in -o 8.out -r 8.crd -p
solhis.top -c solhis.crd -x 8.mdcrd (core dumped)
This is the error message, and output file is
---------------------------------------
GIBBS Version 5 AMBER/UCSF(1997)
--------------------------------------
[-O]verwriting output
File Assignments:
-----------------
|PIN : umb.in
|POUT : 8.out
|PCOORD : 8.mdcrd
|PVEL : PVEL
|PEN : PEN
|PPARM : solhis.top
|PINCRD : solhis.crd
|PREFC : PREFC
|PREST : 8.crd
|PINFO : PINFO
|MICSTAT : MICSTAT
|CONSTMAT: CONSTMAT
|CNSTSCRT: CNSTSCRT
|PATNRG : PATNRG
Here is the input file:
FEP two methanes PMF
&cntrl
ntx=1, # no velocity information
ntb=2, # constant pressure
ntp=1, # MD with isotropic position scaling
ntt=5, # constant temparature and
# separate solute/solvent tempature scaling
dt=0.002,
# tautp=0.05,
nstlim=20000,
nstmeq=4000,
nstmul=16000,
temp0=300.0, # reference temparature
ntc=3, # SHAKE all bonds are constrained
ntf=3, # same as NTC
ncorc=1, # constraint energy
cut=9.0,
intprt=0, # no intra-perturbed group
ntpr=100,
ntwx=100,
ntwe=100,
nrun=41,
almda=1.0,
almdel=0.1,
isldyn=-3,
ielper=0,
intr=1, # internal restraints for PMF calculation
scnb=2.0, scee=1.2,
&end
1 6 0 0 1 0 1 1.00000 0.00000
5.00000 8.00000 5.00000 8.00000 0 0
-------------------------------------------------------------------------------
READING MOLECULAR TOPOLOGY FILE (PPARM)
What is the problem?
Thank you for any help.
--
Best wishes,
Myunggi Yi
===========================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL. 32306
(850) 645-1334
http://www.csit.fsu.edu/~myunggi
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Received on Thu Feb 19 2004 - 04:53:00 PST
