Date: Sun, 26 Apr 2026 17:24:38 +0000
Ok thank you so much all , and as well I did change the modeller model of which had better loops not overlapping that much , and I Understood now that the protonation process itself yielded for me hydrogens in non favorable stances and that's why I am having these warnings, but to be sure could minimization be quite effective to sort it out like in docking prep for example ? excuse me for such question as I am new and learning still.
Abdulrahman Walid Attia Ibrahim ElBagoury
Antivirale und Antivirulenz-Wirkstoffe
Helmholtz-Institut f?r Pharmazeutische Forschung Saarland
University Campus E8.1, 66123 Saarbr?cken
[cid:Helmholtz_Submarke_HIPS_DE_RGB_ab888326-d1f3-4691-8fd5-14b7f77ded78.jpg]<https://www.helmholtz-hips.de/de/>
Ein Standort des Helmholtz-Zentrums f?r Infektionsforschung GmbH (HZI), Braunschweig, in Kooperation
mit der Universit?t des Saarlandes
________________________________
Helmholtz-Zentrum f?r Infektionsforschung GmbH | Inhoffenstra?e 7 | 38124 Braunschweig | www.helmholtz-hzi.de
Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium f?r Forschung, Technologie und Raumfahrt
Stellvertreter: MinDirig R?diger Eichel, Nieders?chsisches Ministerium f?r Wissenschaft und Kultur
Wissenschaftlicher Gesch?ftsf?hrer: Prof. Dr. Josef Penninger - Administrativer Gesch?ftsf?hrer: Christian Scherf
Gesellschaft mit beschr?nkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477
Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/ <https://www.helmholtz-hzi.de/de/service/datenschutz/>
________________________________
From: Thomas Cheatham <tec3.utah.edu>
Sent: Friday, April 24, 2026 10:36:52 PM
To: AMBER Mailing List
Cc: ElBagoury, Abdulrahman Walid Attia Ibrahim
Subject: Re: [AMBER] [EXTERN] Re: Need help in proceeding with md sim
> > 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
/-\
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
(image/jpeg attachment: Helmholtz_Submarke_HIPS_DE_RGB_ab888326-d1f3-4691-8fd5-14b7f77ded78.jpg)
