I'm not sure what you mean by "number of dihedrals". Can you
be specific as to what value in the prmtop you are using for this?
Is it dihedrals involving hydrogen, not involving hydrogen, or number
of dihedral types, etc. one complication that you may already understand
is that dihedrals are given pointers to dihedral types, which actually
have the parameters. it's not surprising that the number of types doesn't
sum up, since some may be shared. the actual numbers themselves
(such as NPHIH, MPHIA) should sum up fine.
if your program can extract part of the prmtop to make a new prmtop,
can you compare the dihedrals listed in each prmtop and find out
which ones differ?
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
Petr Kulhanek wrote:
>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.chemi.muni.cz
>##########################################
>
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Received on Fri Oct 08 2004 - 14:53:00 PDT
