AMBER Archive (2003)

Subject: AMBER: gibbs pmf calculation

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Wed Aug 20 2003 - 14:24:29 CDT

Hi:
   I want to use gibbs to do a pmf calculation. But I always get this
error message:

gibbs -O -i gibbs.in -o gibbs.out -p dhna-hp-tar.prmtop -c temp.restrt
-r gibbs1.restrt -x gibbs.crd -e gibbs.ene -ms gibbs.ms &
[1] 11470
fmt: read unexpected character
apparent state: unit 5 named gibbs.in
last format: (F10.0,10I5)
lately reading sequential formatted external IO

[1] Abort gibbs -O -i gibbs.in -o gibbs.out
-p dhna-hp-tar.prmtop -c temp.restrt -r ... (core dumped)

This is the output I get:

          ---------------------------------------
          GIBBS Version 5 AMBER/UCSF(1997)
          --------------------------------------

  [-O]verwriting output
 File Assignments:
 -----------------

|PIN : gibbs.in
|POUT : gibbs.out
|PCOORD : gibbs.crd
|PVEL : PVEL
|PEN : gibbs.ene
|PPARM : dhna-hp-tar.prmtop
|PINCRD : temp.restrt
|PREFC : PREFC
|PREST : gibbs1.restrt
|PINFO : PINFO
|MICSTAT : gibbs.ms
|CONSTMAT: CONSTMAT
|CNSTSCRT: CNSTSCRT
|PATNRG : PATNRG

Here is the input file:

&cntrl
ntx=5,
ntb=0,
ntt=1,
temp0=300.0,
dt=0.002,
nstlim=10000,
nstmeq=3000,
nstmul=7000,
ntc=2,
ntf=2,
cut=999.0,
ntpr=100,
ntwx=100,
ntwe=100,
nrun=11,
almda=1.0,
almdel=0.1,
isldyn=-3,
ielper=0,
intr=1,
&end
15468, 1155, 0, 0, 1, 0, 0, 1.00000, 0.50000
1000.00000, 3.50000,1000.00000, 8.00000, 0, 0
15468, 1155, 0, 0, 1, 0, 0, 0.40000, 0.00000
1000.00000, 8.50000,1000.00000, 20.00000, 0, 0

-------------------------------------------------------------------------------

                   READING MOLECULAR TOPOLOGY FILE (PPARM)

   Basically it stops when reading topology file. Can anyone tell me
what is wrong? Thanks.

Lishan 

-- 
Lishan Yao <yaolisha_at_pilot.msu.edu>
MSU

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