AMBER Archive (2004)

Subject: AMBER: problems with dihedrals

From: Petr Kulhanek (kulhanek_at_chemi.muni.cz)
Date: Fri Oct 08 2004 - 07:53:03 CDT

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

##########################################
 RNDr. Petr Kulhanek
 National Centre for Biomolecular Research
 Faculty of Science, Masaryk University Brno
 Kotlarska 2, 611 37 Brno, Czech Republic
 e-mail: kulhanek_at_chemi.muni.cz
##########################################

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