[AMBER] Leap : problem with copying and combining DNA items

From: Jérémie Knoops <jeremie.knoops.gmail.com>
Date: Mon, 8 Jun 2015 08:58:18 +0200

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.


Jérémie Knoops
Ma2 Student

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Received on Mon Jun 08 2015 - 00:00:03 PDT
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