Date: Thu, 4 Nov 2021 17:07:41 +0000
Dear AMBER experts,
The periodic water box is corrupted by minimization procedure.
See scripts and figures below.
I need your advice how to resolve the problem.
Thank you,
Michael
The initial system (protein in water box) was generated by
the tleap.in script:
source leaprc.protein.ff14SB
source leaprc.water.tip3p
mc = loadpdb protein_nh.pdb
solvateBox mc TIP3PBOX 16
addIonsRand mc Na+ 296 Cl- 308
saveAmberParm mc mc.prmtop mc.inpcrd
quit
The next step was the water minimization only,
restraining the protein by min1.in script:
Minimize water
System minimization:
&cntrl
imin=1, ntmin=1, nmropt=0, drms=0.1
maxcyc=20000, ncyc=1500,
ntx=1, irest=0,
ntpr=100, ntwr=100, iwrap=0,
ntf=1, ntb=1, cut=8.0, nsnb=20,
igb=0,
ibelly=0, ntr=1,
restraintmask="!:WAT", restraint_wt=10.0,
&end
/
[cid:d0b8a807-cb5f-46b3-a980-2d3e2ae46f6b]
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
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