Dear Amber List members,
I have been running production MD simulation of non-covalent enzyme
–peptide
substrate (SVLAKEL) complex by Amber14 with ff14sb force field in periodic
water box.
I used restraints on two interatomic distances (RST.dist file) in order to
keep
biochemically reasonable position of catalytic residues and substrate.
Suddenly,
at 31 ns snapshot I have observed irrelevant isomerization at the A-K
(Ala-Lys)
amide bond of peptide substrate backbone where carbonyl bond of Ala became
in cis position to N-H amide bond of Lys.
In order to fix the problem I have added torsional restraint on the
problematic
amide bond (rst.bb file) and restarted MD from 30 ns snapshot with correct
trans isomer of the target amide bond. Unfortunately, I found again
incorrect cis
isomer at 31 ns on this amide bond.
It seems that there is an error in my md3.in and rst.bb files.
See below listings of the files.
I would appreciate your help.
Thank you,
Michael
*md4.in <
http://md4.in>*
30 ns production phase MD
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 1.0,
cut = 10.0, ntr = 0, iwrap = 1,
ntc = 2, ntf = 2,
tempi = 310.0, temp0 = 310.0,
ntt = 3, gamma_ln = 0.5,
nstlim = 15000000, dt = 0.002,
ntpr = 5000, ntwx = 5000, ntwr = 5000, ig = -1,
nmropt=1,
/
&wt type='END' /
DISANG= ../RST.dist
LISTOUT=POUT
/
DISANG1= ../rst.bb
LISTOUT=POUT
/
*RST.dist*
&rst
ixpk= 0, nxpk= 0, iat=1030,1692, r1= 1.30, r2= 1.80, r3= 2.80, r4= 3.30,
rk2=50.0, rk3=50.0, ir6=1, ialtd=0,
&end
&rst
ixpk= 0, nxpk= 0, iat=1030,61, r1= 1.30, r2= 1.80, r3= 3.00, r4= 3.50,
rk2=50.0, rk3=50.0, ir6=1, ialtd=0,
&end
*rst.bb <
http://rst.bb>*
&rst
iat=36,51,53,55, r1=0., r2=180., r3=180., r4=360.,
rk2 = 35., rk3 = 35., /
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
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Received on Sun Jul 26 2015 - 09:30:02 PDT
