Dear AMBER users,
Dear Jason,
Is this issue fixed?
Otherwise, what is the easiest method to create parameters and
topology files for MD simulations in explicit solvent (DNA, ligand and
DNA+ligand) followed by a MM-GBSA analysis (separate trajectory
approach)?
I don't know how to create them easily without using the combine command.
Thanks,
Jérémie Knoops
2015-06-08 8:58 GMT+02:00 Jérémie Knoops <jeremie.knoops.gmail.com>:
> Dear amber users,
>
> I came across the following problem in leap (ambertools 12 or 14) : two
> parameter files, one created from a DNA unit and one from his copy contain a
> different number of NPHIH (Number of torsions containing Hydrogen).
> For example :
>
> source leaprc.ff12SB
> DNA = sequence { DT5 DT DT3 }
> DNA2 = copy DNA
> saveoff DNA DNA.lib
> saveamberparm DNA DNA.prmtop DNA.inpcrd
> saveoff DNA2 DNA2.lib
> saveamberparm DNA2 DNA2.prmtop DNA2.inpcrd
>
>
> There is one more NPHIH in the parameter file created from the copied unit
> (DNA2.prmtop) than in the file from the loaded unit(DNA.prmtop). It is very
> difficult to see which one is the good one because the dihedrals numbering
> is completely different. If there is a good one...
> I made some tests and I had not the same problem with proteins or small
> molecules, the problem only occurs with DNA. It also occured when I loaded
> NAB-created pdb files.
>
> More interestingly, when I combine them with a small ligand (mol2 file
> created with R.E.D. server dev. or antechamber) to create "complexes", it's
> now the parameter file of the complex created with the loaded unit
> (DNA-LIG.prmtop) which contains one NPHIH more than the one from the copy
> (DNA-LIG2.prmtop) !
>
> LIG = loadmol2 Mol-sm_m9-c1.mol2
> DNA-LIG= combine {DNA LIG}
> saveoff DNA-LIG DNA-LIG.lib
> saveamberparm DNA-LIG DNA-LIG.prmtop DNA-LIG.inpcrd
> DNA-LIG2= combine {DNA2 LIG}
> saveoff DNA-LIG2 DNA-LIG2.lib
> saveamberparm DNA-LIG2 DNA-LIG2.prmtop DNA-LIG2.inpcrd
>
> The number of NPHIH of the complex is expected to be the sum of the NPHIH of
> the DNA and the NPHIH of the ligand, but it is not the case here.
>
>
> DNA-LIG 207 DNA-LIG2 206
> DNA 179 DNA2 180
> LIG 27 LIG 27
> Delta +1 Delta -1
>
> If the file for the DNA created from one unit is a correct file, the file
> for the complex from the same unit is probably wrong!
> That is actually the problem that I noticed when I tried multiple trajectory
> MM-GBSA.
> So I would like to know which parameter files I could use to start the
> dynamics and to perform multiple trajectory MM-GBSA.
>
> Thanks
>
> Jérémie Knoops
> Ma2 Student
> UMons
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Received on Mon Oct 05 2015 - 06:00:05 PDT
