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From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Sent: Thursday, December 5, 2019 6:00:34 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject:
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Amber 18 PMEMD 2018
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| PMEMD implementation of SANDER, Release 18
| Run on 12/05/2019 at 17:49:51
| Executable path: /usr/local/amber18/bin/pmemd.cuda
| Working directory: /home /TI_setup/complex/EQUIL/0.08198
| Hostname: cluster1
[-O]verwriting output
File Assignments:
| MDIN: equil1A.in
| MDOUT: complex_equil1A.out
| INPCRD: complex_heat3.rst
| PARM: complex_WAT.prmtop
| RESTRT: complex_equil1A.rst
| REFC: complex_WAT.inpcrd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: complex_equil1A.mdcrd
| MDINFO: mdinfo
| MDFRC: mdfrc
Here is the input file:
&cntrl
imin = 0, nstlim = 1000000, dt = 0.002,
irest = 1, ntx = 5, ig = -1,
tempi = 300.0, temp0 = 300.0,
ntc = 2, ntf = 1, tol = 0.00001,
taup = 1,
ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 10.0, iwrap = 1,
ntt =3, ntb = 2, ntp = 1, gamma_ln=1.0,
nscm = 0,
ntr=1, restraintmask=':287', restraint_wt=100,
icfe = 1, clambda = 0.08198, ifsc=1,
timask1=':C3N',timask2='',
/
Note: ig = -1. Setting random seed to 591171 based on wallclock time in
microseconds.
| irandom = 1, using AMBER's internal random number generator (default).
Error message!
5. REFERENCE ATOM COORDINATES
default name
Mask :287; matches 6 atoms
TI Mask 1 :C3N; matches 6 atoms
TI Mask 2 matches 0 atoms
TI region 1: 43837 atoms
TI region 2: 43831 atoms
ERROR: The number of linearly scaled atoms must be the same, check timask1/2 and scmask1/2
Why is it considering linear scaling? I have ifsc>0 (for soft core potentials) in my input file , do I have to explicitly mention value of klambda =4 or 5 as because the default value is 1.
But page 424 of the Manual says $B!H(BWe have found that setting k= 6 with disappearing groups as large as tryptophan works, but using the softcore option (ifsc>0) instead is generally preferred.[447] Note that the behavior of h$B"_(BV/$B"_(B $B&K(Bi as a function of $B&K(B is not monotonic when klambda > 1. You may need a fairly fine quadrature to get converged results for the integral, and you may want to sample more carefully in regions where h$B"_(BV/$B"_(B $B&K(Bi is changing rapidly$B!D!I(B
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Received on Thu Dec 05 2019 - 15:30:02 PST
