Agree. I say refine your pdb4amber with modeller (salilab) to rule out
steric clashes, then solvate/build with TLeap. Simulate a few nanoseconds
(always on explicit solvent). Run on triplicate. Compare. See what comes
out.
On Fri, Apr 24, 2026, 22:37 Thomas Cheatham via AMBER <amber.ambermd.org>
wrote:
>
> > > so what could be your recommendation ? is there a way to adjust for the
> > > close contacts ?
> >
> > Don't be afraid to experiment. A short (say 100 step) minimization using
> > sander with ntmin=3 and some constraints (ntr=1) on non-hydrogen atoms
> > should tell you a lot.
>
> I also try a first minimization with electrostatics turned off; if
> there are overlapping atoms of opposite charge, charge wins over vdw and
> the opposite charges may/will collapse leading to failure.
>
> <notchpeak1 1029> more
> ../cheatham-group4/DNA/research/G-DNA/3ibk/inputs/min_noelec.in
> production
> &cntrl
> imin = 1, maxcyc = 300, ncyc = 300,
> ntb = 2, ntp = 1,
> cut = 9.0,
> iwrap = 1,
> lastist = 10000000,
> lastrst = 10000000,
> nmropt = 1,
> &end
> &wt
> type = 'ELEC', value1 = 0.0,
> &end
> &wt
> type = 'END',
> &end
> DISANG=inputs/restraints.in
> LISTOUT=POUT
>
> <notchpeak1 1030> more ../cheatham-group4/DNA/research/G-DNA/3ibk/inputs/
> restraints.in
> &rst iat = 0, &end
>
> Good luck --tec3
>
> \-/ Professor Thomas E. Cheatham, III
> -/- Department of Medicinal Chemistry, College of Pharmacy
> /-\
> \-/ tec3.utah.edu http://www.chpc.utah.edu/~cheatham
> -/- SKH-4914 (801) 587-9652
> /-\
>
>
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Received on Fri Apr 24 2026 - 18:00:02 PDT
