AMBER Archive (2004)

Subject: AMBER: pmf calculation using gibbs.

From: Myunggi Yi (my02c_at_fsu.edu)
Date: Wed Feb 18 2004 - 23:22:46 CST

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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