Dear Amber Community,
I did MM/PBSA analysis of protein + ligand complex from single trajectory
and I found that the dihedral energy contribution to interaction energy was
not zero. So I tried to locate the stage from the mistake or mistakes could
come and I found out that the ligand topology contains different number of
dihedrals than the same part in complex topology.
Thefore I prepared toplogies once again with the exactly same order of prep
and parameter files in tleap using following script:
----------------------------------------------------------------------------
--------
source leaprc.ff99
loadamberparams glycam_2000a.dat
loadamberparams mangan.dat
loadamberparams pyr.dat
loadamberprep la.prep
loadamberprep mangan.prep
loadamberprep pyr.prep
loadamberprep uracil.prep
loadamberprep deoxylac.prep
COMPLEX=loadpdb complex.pdb
desc COMPLEX.285
desc COMPLEX.286
bond COMPLEX.285.1 COMPLEX.286.1
saveamberparm COMPLEX complex.top complex.crd
PROTEIN=loadpdb protein.pdb
desc PROTEIN.285
desc PROTEIN.286
bond PROTEIN.285.1 PROTEIN.286.1
saveamberparm PROTEIN protein.top protein.crd
LIGAND=loadpdb ligand.pdb
saveamberparm LIGAND ligand.top ligand.crd
quit
----------------------------------------------------------------------------
-------
The results are as follows:
Number of dihedrals Dihedral energy
protein 16957 2308.3250
ligand 168 7.8991
sum 17125 2316.2241
---------------------------------------------------------
complex 17118 2316.1308
======================================
difference 7 0.0933
The results confirm that the ligand contains different number of dihedrals
which results to non-zero dihedral energy contribution to interaction
energy.
To bring more light in my problem I wrote program which is capable to
extract any part from topology as new one. If I use ligand topology
(ext_ligand) which is extracted by this program from complex topology the
results are now correct.
Number of dihedrals Dihedral energy
protein 16957 2308.3250
ext_ligand 161 7.8058
sum 17118 2316.1308
---------------------------------------------------------
complex 17118 2316.1308
======================================
diff 0 0.0000
Unsolved question for me is 'how is it possible that the the number of
dihedrals of some individual molecule depends on the rest of system?'.
Some additional notes:
tleap from AMBER 8 distribution was used.
The other aditive energy contributions to interaction energy (bond and
angle) are zero in all cases.
Ligand is deoxylactose and protein contains galactosyl-UDP.
All files related to this problem can be downloaded from:
http://www.ncbr.chemi.muni.cz/~kulhanek/downloads/top_tests.tar.gz
Thanks in advance for any answer,
Petr Kulhanek
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RNDr. Petr Kulhanek
National Centre for Biomolecular Research
Faculty of Science, Masaryk University Brno
Kotlarska 2, 611 37 Brno, Czech Republic
e-mail: kulhanek.chemi.muni.cz
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Received on Fri Oct 08 2004 - 14:53:00 PDT
