Hi there,
I have this molecule ATP, deprotonated, with 46 atoms and -1 net charge
which topology was generated via Antechamber.
I tested with sander, namd and gromacs (converting it via ACPYPE). The
latter is not discussed here although the general result is similar to the
former 2.
Essentially I am doing a energy minimisation (EM) following these
instructions (set only to emphasise the issue, not really for production):
#AMBER 11
cat << EOF >| mdin
Minimization
&cntrl
imin=1, maxcyc=2000,
ntmin=2,
ntb=0,
igb=0,
cut=999,
/
sander -O -i mdin -o mdout -p HATP_AC.prmtop -c HATP_AC.inpcrd
ambpdb -p HATP_AC.prmtop < restrt > HATP_amber.pdb
mdout OUTPUT:
NSTEP ENERGY RMS GMAX NAME NUMBER
1950 -2.2514E+08 5.9075E+13 3.4193E+14 O01 4
BOND = 35.0839 ANGLE = 124.4508 DIHED =
28.9012
VDWAALS = -8.5795 EEL = 933.8418 HBOND =
0.0000
1-4 VDW = 15.4554 1-4 EEL = ************* RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 -1.3381E+07 2.0866E+11 1.2077E+12 HHO 1
BOND = 35.0845 ANGLE = 124.4511 DIHED =
28.9012
VDWAALS = -8.5795 EEL = 933.8418 HBOND =
0.0000
1-4 VDW = 15.4554 1-4 EEL = ************* RESTRAINT =
0.0000
# NAMD 2.7b2
cat << EOF >| HATP_namd.conf
outputEnergies 50 # Energy output frequency
DCDfreq 2 # Trajectory file frequency
timestep 2 # in unit of fs
temperature 300 # Initial temp for velocity assignment
cutoff 999
switching off # Turn off the switching functions
PME off # Use PME for electrostatic calculation
amber on # Specify this is AMBER force field
parmfile HATP_AC.prmtop # Input PARM file
ambercoor HATP_AC.inpcrd # Input coordinate file
outputname HATP_namd # Prefix of output files
exclude scaled1-4
1-4scaling 0.833333 # =1/1.2, default is 1.0
minimize 2000
EOF
namd2 +p2 HATP_namd.conf >| namd.log
LINE MINIMIZER BRACKET: DX 1.29731e-05 1.06277e-05 DU -1.70323e-05
1.14306e-05 DUDX -2.62589 5.05233e-05 2.15101
LINE MINIMIZER REDUCING GRADIENT FROM 44.7384 TO 0.0447384
TIMING: 2000 CPU: 0.76958, 0.000377574/step Wall: 0.423322,
0.00021419/step, 0 hours remaining, 98.023438 MB of memory in use.
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL TOTAL3
TEMPAVG
ENERGY: 2000 31.2774 272.2172 33.5413 0.0000
-2823.3313 23.6328 0.0000 0.0000
0.0000 -2462.6627 0.0000 -2462.6627 -2462.6627
0.0000
vmd -parm7 HATP_AC.prmtop -rst7 HATP_AC.inpcrd HATP_namd.dcd
I tried but I wish I could set the parameters in namd and sander so the
energy results could be closer. Anyway what's happening is that atoms O01
and HHO in the phosphate have opposite charges and they are 1-4 neighbours
so after EM the Hydrogen collapse over the Oxygen (see the 1-4 EEL energies
from sander mdout).
With NAMD and VMD and I can reproduce and visualise this same issue (happens
with Gromacs as well).
I understand that in Amber 1-4 interactions are there although scaled down
by a factor. What I just want to understand is if such a behaviour would be
expected (although being more like an artefact) considering the peculiarity
of the ATP molecule. And why vdW repulsion is not (apparently) acting here?
I attached HATP_amber.pdb, generated from the last frame of sander EM.
Thanks in advance,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Tue Jun 15 2010 - 04:30:05 PDT
