Hello,
I overcame the problem of Belly + distance restraints. It was
because I set the option ntr=1 along with ibelly=1. When I removed ntr
option, and used the following mdin, the MD started (and seems to be
working) ( Note: &end was replaced with / as I am using IBM SP3).
Thanks for all those who provided feedback.
Sincerely,
-Sanjeev
-------------------------mdin----------------------------
Restraint improvement attempt
&cntrl
imin=0,
nmropt=1,
ibelly=1,
ntx=1, irest=0, t=30.,
ntpr=50, ntwr=500, iwrap=1, ntwx=500, ntwe=50,
ntf=2, ntb=1, igb=0, scnb=2.0, scee=1.2,
cut=12.0,
nstlim=5000, ndfmin=6, ntcm=1, dt=0.002,
tempi=000., temp0=300., ntt=1, tautp=0.5, dtemp=0.,
ntp=0, taup=0.5, npscal=1,
ntc=2, tol=0.00001,
vlimit=10.,
/
&ewald
vdwmeth=1,
/
&wt type ='TEMP0',istep1=0, istep2=1500,
value1=10., value2=500.,
/
&wt type ='TEMP0',istep1=1501, istep2=5000,
value1=500., value2=300.,
/
&wt type ='TAUTP',istep1=0, istep2=1500,
value1=0.20, value2=0.20,
/
&wt type ='TAUTP',istep1=1501, istep2=3500,
value1=4.00, value2=2.00,
/
&wt type ='TAUTP',istep1=3501, istep2=4500,
value1=1.00, value2=0.50,
/
&wt type ='TAUTP',istep1=4501, istep2=5000,
value1=0.05, value2=0.05,
/
&wt type ='END'
/
&wt type ='END'
/
&rst iat=258, 2198, r1=2.5, r2=2.7, r3=3.2, r4=3.5, rk2=25., rk3=25.,
/
&rst iat=258, 2194, r1=2.5, r2=2.7, r3=3.2, r4=3.5, rk2=25., rk3=25.,
/
&rst iat=649, 2189, r1=2.5, r2=2.7, r3=3.2, r4=3.5, rk2=25., rk3=25.,
/
&rst iat=649, 2194, r1=2.5, r2=2.7, r3=3.2, r4=3.5, rk2=25., rk3=25.,
/
&rst iat=2080,2198, r1=2.5, r2=2.7, r3=3.2, r4=3.5, rk2=25., rk3=25.,
/
&rst iat=2090,2198, r1=2.5, r2=2.7, r3=3.2, r4=3.5, rk2=25., rk3=25.,
/
&rst iat=700, 2189, r1=2.5, r2=2.7, r3=3.2, r4=3.5, rk2=10., rk3=10.,
/
&rst iat=710, 2186, r1=2.5, r2=2.7, r3=3.2, r4=3.5, rk2=10., rk3=10.,
/
&rst IAT=0,
/ Residues allowed to move (ie, all excluding the protein) RES 134 2490
END END LISTOUT=POUT
Received on Sat Sep 08 2001 - 04:24:37 PDT
