Dear amber community,
I have been having a difficulty trying to
figure out why I keep getting totally inconsistent
absolute G results out of mm_gbsa runs for the
following
tri- (pH 6.5) and di-(pH 7.4) protonated states of an
aminoglycoside ligand core (ligand a and b,
respectively).
NH3+
CH2 NH2
CH--O CH--CH2
HOCH CH--CH CH-NH3+
CH--CH CH--CH
OH NH3+ OH OH
Ligand a (pH 6.5)
NH3+
CH2 NH2
CH--O CH--CH2
HOCH CH--CH CH-NH3+
CH--CH CH--CH
OH NH2 OH OH
Ligand b (pH 7.4)
Although sander seems to have done a pretty good job
on restraining
ligand a and b in implicit water based on my NOE and
3JHH NMR
data, stand-alone (stability) mm_gbsa results for the
final
snapshots of the MD runs (for ligand a and b) indicate
that
ligand a is favorable (negative G) while ligand b is
unfavorable
(positive G). Whereas, my NMR data strongly suggest
that those
two charged states of the ligand above do exist in
solution
in different conformations at different pH.
So, I would expect to get a more rational (at least
negative)
absolute G value for ligand b as well, but this does
not seem
to be the case with mm_gbsa. Why?
Nevertheless, nmode runs for final MD snapshots of
Ligand a and b
resulted in entropy values pretty much as I expected.
Here is what I have done to carry out mm_pbsa and
nmode computations:
First of all, I created AM1-BCC charges for ligand a
and b in mol2 format by
antechamber as follows:
Ligand a:
antechamber -i nea65.amb.pdb -fi pdb -o nea65.mol2 /
-fo mol2 -at gaff -c bcc -rn NEA -nc 3 -j 5
Ligand b:
antechamber -i nea74.amb.pdb -fi pdb -o nea74.mol2 /
-fo mol2 -at gaff -c bcc -rn NEA -nc 2 -j 5
I then generated prmtop and incrd files for ligand a
and b in tleap as follows:
tleap -f leaprc.gaff
nea = loadmol2 nea65(/74).mol2
set default gibbs off
set default pbradii mbondi
saveamberparm nea nea65(/74).prmtop nea65(/74)-start.x
quit
Afterwards, I pre-minimized the ligands before MD runs
as follows:
sander -O -i minrelax.in -o nea65(/74).minrelax.out /
-c nea65(/74)-start.x -p nea65(/74).prmtop /
-r nea65(/74).minrelax.x
where minrelax.in is
&cntrl
imin=1, maxcyc=2000, ncyc=250, cut=15, ntpr=50, ntb=0,
igb=1
/
After I relaxed the ligands, I executed sander as
follows
sander -O -i mdnmr.in -o nea65(/74).mdnmr.out /
-c nea65(/74).minrelax.x -p nea65(/74).prmtop /
-r nea65(/74).mdnmr.x -x nea65(/74).mdnmr.traj
where mdnmr.in is
&cntrl
imin=0, ntb=0, igb=1, nstlim=15000, pencut=-0.001,
nmropt=1, ntpr=10, ntwx=10, t=298.15, ntt=3,
gamma_ln=1.0,
tempi=0, temp0=298.15, dt=0.001, cut=15.0, vlimit=5
/
&wt type='REST', istep1=0,istep2=5000,value1=0.1,
value2=1.0, /
&wt type='REST', istep1=5001,istep2=15000,value1=1.0,
value2=1.0, /
&wt type='END' /
LISTOUT=POUT
DISANG=RSTpH65(/74)
I then did GB stability computations for the final
coordinates of
the MD runs [nea65(/74).mdnmr.x].
Thus, I renamed the final coordinate files as follows
cp nea65(/74).mdnmr.x nea65(/74).mdnmr_lig.crd.1
so that mm_gbsa reads in only the final state of my MD
runs.
I set temp at 298.15 K in
/home/jenk/amber8/src/mm_pbsa/mm_pbsa_statistics.pm
(line 46)
and then,
I set maxcyc to 0 in
/home/jenk/amber8/src/mm_pbsa/mm_pbsa_createinput.pm
(line 202)
to stop sander minimization for the final ligand
coordinates
after MD runs.
I then executed mm_pbsa.pl as follows
mm_pbsa.pl mm_pbsa.in > mm_pbsa.log
where mm_pbsa.in is
##############################################
.GENERAL
#
PREFIX nea65(/74).mdnmr
PATH ./
#
COMPLEX 0
RECEPTOR 0
LIGAND 1
#
COMPT XXX
RECPT XXX
LIGPT nea65(/74).prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 0
MS 1
#
NM 0
#
##############################################
.MM
#
DIELC 1.0
#
##############################################
.GB
#
IGB 1
GBSA 1
SALTCON 0.00
EXTDIEL 78.5
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
##############################################
.MS
#
PROBE 0.0
##############################################
mm_gbsa results for ligand a and b are
Ligand a:
# MEAN STD
# =======================
ELE 275.22 0.00
VDW 2.11 0.00
INT 65.28 0.00
GAS 342.61 0.00
GBSUR 3.95 0.00
GB -350.11 0.00
GBSOL -346.15 0.00
GBELE -74.88 0.00
GBTOT -3.54 0.00
Ligand b:
# MEAN STD
# =======================
ELE 150.46 0.00
VDW 1.01 0.00
INT 69.61 0.00
GAS 221.08 0.00
GBSUR 3.91 0.00
GB -183.20 0.00
GBSOL -179.29 0.00
GBELE -32.74 0.00
GBTOT 41.79 0.00
Finally, I executed nmode as follows:
nmode -O -i nmode.in -o nea65(/74).nmode.out /
-p nea65(/74).prmtop -c nea65(/74).mdnmr_lig.crd.1 /
-r nea65(/74).nmode.x -ref nea65(/74).mdnmr_lig.crd.1
where nmode.in is
&data
ntrun = 1, nsave=1, cut=99.0, ntx=1,
nprint=1,
drms = 25, maxcyc=0,
scnb=2.0, scee=1.2,
dielc=4, idiel=0,
ismem=1,
&end
Here are the nmode results for ligand a and b;
Ligand a:
E Cv S
kcal/mol cal/mol-kelvin cal/mol-kelvin
------------------------------------------------------
Total 291.251 94.421 226.691
translational 0.888 2.979 43.206
rotational 0.888 2.979 34.835
vibrational 289.475 88.463 148.651
Ligand b:
E Cv S
kcal/mol cal/mol-kelvin cal/mol-kelvin
------------------------------------------------------
Total 283.197 92.348 183.544
translational 0.888 2.979 43.197
rotational 0.888 2.979 34.765
vibrational 281.421 86.390 105.582
As seen above entropic contributions (Total S) to
absolute G are
favorable for both Ligand a and b. That is fine!
Then, why do I get an unfavorable GBTOT value for
Ligand b ?
I have also tried running sander and mm_gbsa with
igb=2 and 5
using default PBradii mbondi2 in tleap, but mm_gbsa
results did not
significantly change either. In all igb cases (1,2 and
5) I kept getting
unfavorable absolute G for Ligand b. However, my NMR
data tell me
that Ligand b does exist in solution with O salt
concentration.
Could someone please let me know
what have I done wrong or what have I been missing
here?
Do additional point parameters help overcome the GBTOT
issue?
regards,
jenk.
Faculty Candidate in Turkey
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Received on Fri Dec 24 2004 - 10:53:00 PST
