Hi all,
I am attempting to perform FEP calculations on a solvated
protein-ligand system. I have used solvent cap option
(IVCAP=0) and moved only the atoms in the vicinity of ligand
(IBELLY=1). Minimization and MD(with the same options as
above) went through alright, but Gibbs reports the folowing
error:
WARNING: SHAKE/TORCON COULD NOT RESET THE COORDINATES.
WILL CONTINUE WILL NON-SHAKEN COORDINATES ON THIS STEP
Routine TORCON (internal constraints) failed
to converge within 1000 iterations.
WARNING: SHAKE/TORCON COULD NOT RESET THE COORDINATES.
MORE THAN 6SHAKE/TORCON RE-TRIES IN A ROW. GIBBS
WILL STOP.
I am attaching the Control data (input) file. I will be
grateful if any one could help.
Regards,
K.Seshadri
School of Biochemistry and Molecular Biology
University of Leeds
Leeds LS2 9JT, U.K.
TITLE: Free energy calculation - Forward
&cntrl
timlim = 0.1000000E+09 , irest = 0 , ibelly = 1 ,
ichdna = 0 , ipol = 0 , i3bod = 0 ,
iewald = 0 ,
ntx = 5 , ntxo = 1 , ig = 71277 ,
tempi = 300.0000 , heat = 0.0000000E+00 ,
ntb = 0 , iftres = 0 , boxx(1)= 0.0000000E+00 ,
boxx(2)= 0.0000000E+00 , boxx(3)= 0.0000000E+00 , betar = 0.0000000E+00 ,
ibxrd = 0 ,
nrun = 21 , ntt = 5 , temp0 = 300.0000 ,
dtemp = 999.0000 , tautp = 0.2000000 , tauts = 0.2000000 ,
isolvp = 0 , nsel = 0 , dtuse = 0.5000000 ,
ntp = 0 , npscal = 0 , pres0 = 1.000000 ,
comp = 44.60000 , taup = 0.6000000 ,
ndfmin = 0 , ntcm = 0 , nscm = -1 ,
istay = 0 , nstay = 0 , isvat = 1 ,
nstlim = 20000 , init = 4 , ntu = 1 ,
t = 0.0000000E+00 , dt = 0.1000000E-02 , vlimit = 10.00000 ,
ivemax = 0 ,
ntc = 3 , ntcc = 0 , nconp = 0 ,
tol = 0.1000000E-09 , tolr2 = 0.1000000E-03 , ncorc = 1 ,
ishkfl = 6 , itimth = 0 , jfastw = 0 ,
ntf = 3 , ntid = 0 , ntn = 3 ,
ntnb = 1 , nsnb = 25 , idiel = 1 ,
inbper = 0 , ielper = -1 , imgslt = 0 ,
idsx0 = 200 , itrslu = 1 , ioleps = 0 ,
intprt = 5 , itip = 0 ,
cut = 8.000000 , scnb = 2.000000 , scee = 2.000000 ,
dielc = 1.000000 , cut2nd = 0.0000000E+00 , cutprt = 0.0000000E+00 ,
ntpr = 20000 , ntwx = -1 , ntwv = -1 ,
ntwe = -1 , ntwxm = 0 , ntwvm = 0 ,
ntwem = 0 , ntpp = 0 , ioutfm = 0 ,
isande = 1 , iperat = 4 , iatcmp = 1 ,
ntatdp = 99999 , icmpdr = 0 , ncmpdr = 0 ,
ntwprt = 0 , ntwpr0 = 0 ,
ntr = 0 , nrc = 0 , ntrx = 1 ,
taur = 0.1000000 , intr = 0 , ibigm = 1 ,
nmrmax = 0 , iwtmax = 0 , isftrp = 0 ,
rwell = 4.000000 ,
iftime = 0 , ctimt = 40.00000 , almda = 1.000000 ,
almdel = 0.5000000E-01 , isldyn = -3 , idifrg = 1 ,
nstmeq = 10000 , nstmul = 10000 , ndmpmc = 0 ,
idwide = 0 , ibndlm = 0 ,
iavslp = 8 , iavslm = 2 , islp = 0 ,
corrsl = 0.8000000 , amxmov = 0.1000000E-01 ,
iavdel = -1 , iavdem = 2 , amxdel = 0.1000000 ,
almdl0 = 0.1000000E-02 , dlmin = 0.1000000E-04 , dlmax = 0.1000000E-01 ,
amxrst = 0.9999999E-01 , norsts = 0 , ntsd = 0 ,
almstp = -1.000000 ,
nstpe = 10000 , nstpa = 10000 , dte = 0.1000000E-02 ,
dta = 0.1000000E-02 ,
ivcap = 0 , natcap = 0 , fcap = 1.500000 ,
&end
Group input for Belly - List of moving residues
RES 5 5
RES 10 10
RES 12 12
RES 15 15
RES 17 17
RES 19 33
RES 36 47
RES 51 58
RES 67 73
RES 78 94
RES 101 108
RES 114 121
RES 134 134
RES 151 151
RES 161 161
RES 164 164
RES 166 166
RES 262 262
END
END
FEP Components each solute res. sep group
RES -1 157
END
water
RES 158 9999
END
END
Received on Thu Jun 29 2000 - 06:54:22 PDT
