Dear Amber users,
I work on the relative binding free energy calculation using TI of Amber20. I set up the structures of two ligands with as much overlapping of their structures and coordinates as possible, then build the lib files, and frcmod files. When I overlapped those two ligands, they are only different in atoms 34, 42, and 59-64 with the pse file attached. The extra 8 atoms formed two methyl groups and they are physically faraway. In the decharge/ directory, I have the heat.in file as shown below.
heating
&cntrl
imin = 0, nstlim = 10000, irest = 0, ntx = 1, dt = 0.002,
ntt = 1, temp0 = 300.0, tempi = 50.0, tautp = 1.0,
ntc = 2, ntf = 1,
ntb = 1,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 5000,
nmropt = 1,
ntr = 1, restraint_wt = 5.00,
restraintmask='!:WAT & !.H=',
icfe = 1, clambda = 0.0, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':1', timask2 = ':2',
ifsc = 0, crgmask = ':2.34,42,59-64',
/
&ewald
/
&wt
type='TEMP0',
istep1 = 0, istep2 = 8000,
value1 = 50.0, value2 = 300.0
/
&wt type = 'END'
/
But I got error message when I ran it:
vlimit exceeded for step 0; vmax = 73.7945
vlimit exceeded for step 1; vmax = 34.6085
vlimit exceeded for step 3; vmax = 31.1985
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 4 2 38 10
I am wondering where is wrong and how to fix it. Thank you very much.
LZ
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Received on Sun Aug 21 2022 - 05:30:03 PDT
