Dear Ambers,
I solved the problem by replacing residue name,
i.e. WAT -> SPF..
c.f.
http://archive.ambermd.org/201209/0316.html
Thanks.
IK
-----Original Message-----
From: kurisaki [mailto:kurisaki.ncube.human.nagoya-u.ac.jp]
Sent: Monday, April 29, 2013 12:19 PM
To: 'AMBER Mailing List'
Subject: [AMBER] Prepare PRMTOP file for off-SHAKE simulation
Dear Amber Developers and users,
I prepare PRMTOP file to simulate without setting SHAKE.
However, the simulation itself does not work with following error messages.
For pmemd.MPI
> Fast 3-point water residue, name and bond data incorrect!
For sander.MPI
> Error: A residue defined as a "fast 3-point water"
> is not defined by a triangle of three bonds.
> Residue 3 contains 2 bonds.
I made PRMTOP file by using the following tLEaP script.
=========================================================
=========================================================
source leaprc.ff99SB
a = sequence{NALA CALA}
WAT = SPF
loadAmberParams frcmod.spcfw
set default FlexibleWater on
solvateBox a SPCFWBOX 15
saveAmberParm a ALA2_FLX.prmtop ALA2_FLX.prmcrd
quit
=========================================================
=========================================================
And I used the following Amber Input file for simulation.
=========================================================
=========================================================
Molecular Dynamics
&cntrl
TIMLIM = 999999, IMIN = 0,
NTX = 1, IREST = 0, NTRX = 1,
NTXO = 1, NTPR = 1000, NTWR = 0, IWRAP = 0,
NTWX = 1000,
NTB = 1,
CUT = 9.0,
NSTLIM = 10000, NSCM = 1000,
T = 0.0000, DT = 0.00100,
TEMP0 = 1.000, TEMPI = 0.0001, IG = -1,
NTT = 3, gamma_ln = 1.0,
NTP = 0,
NTF = 1, NTC = 1, TOL = 0.000001,
=========================================================
=========================================================
I am most grateful if you give me some advice to resolve the problem.
Yours sincrerly,
Ikuo KURISAKI
P.S.
I use AmberTools 1.4 and Amber12 for these purposes.
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Received on Sun Apr 28 2013 - 21:30:02 PDT
