On Wed, Mar 17, 2021, richa anand wrote:
>
>home/researchscholler/AMBER/amber20_src/bin/teLeap: Warning!
>There is a bond of 5.736 angstroms between C and N atoms:
>------- .R<GLY 67>.A<C 6> and .R<LYS 68>.A<N 1>
You should examine the source of these errors. Amber will create a bond
between residues, and force them to come together. Be sure that is what you
want.
>
>/home/researchscholler/AMBER/amber20_src/bin/teLeap: Warning!
>There is a bond of 7.456 angstroms between C and N atoms:
>------- .R<PRO 97>.A<C 13> and .R<ILE 98>.A<N 1>
>
>/home/researchscholler/AMBER/amber20_src/bin/teLeap: Warning!
>There is a bond of 6.297 angstroms between C and N atoms:
>------- .R<CYS 243>.A<C 10> and .R<LYS 244>.A<N 1>
>
>/home/researchscholler/AMBER/amber20_src/bin/teLeap: Warning!
>There is a bond of 5.725 angstroms between C and N atoms:
>------- .R<PRO 570>.A<C 13> and .R<LYS 571>.A<N 1>
>
>/home/researchscholler/AMBER/amber20_src/bin/teLeap: Note.
>Ignoring the warnings from Unit Checking.
>
>proceeding with these warnings for minimization with input :
>
>&cntrl
>imin=1, maxcyc=10000,ncyc= 5000, cut=8.0, igb=0, ntb=1, ntp=0, ntpr=100,
> /
>
>I obtained TOTAL SIZE OF NONBOND LIST = 19504477.
>
>further proceeding for MD with input file:
>
>
> &cntrl
> imin = 0,
> ntx = 5, irest = 1,
> ntpr = 500, ntwr = 1000, ntwx = 500, ntwe = 500, iwrap = 1
> ntf = 2, igb = 0,
> cut = 10.0,
> nstlim = 5000, dt = 0.002,
> tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 0.5,
> ntb = 2, ntp = 1, taup = 1.0
> ntc = 2, tol = 0.00001,
> vlimit = -1.0d0,
> ioutfm=1,
> /
> &ewald
> vdwmeth = 1,
> /
This is clearly not your first MD run. Look carefully at the minimization
output, and at the mdout files for the earlier MD steps. You are looking
for any signs of errors: minimization did not seem to (roughly) convervge,
tmperature in MD seemed funny, etc.
A good protocol for preparing systems for stable simulations is given
here, which may help:
%A D.R. Roe
%A B.R. Brooks
%T A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations
%J J. Chem. Phys.
%V 153
%P 054123
%D 2020
...good luck...dac
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Received on Wed Mar 17 2021 - 07:00:03 PDT
