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

From: Jason Swails <>
Date: Mon, 8 Jun 2015 08:19:12 -0400

I'm seeing the same thing you are (with the first example, haven't tried
the other). Something is definitely wrong.

I will investigate what's happening here and report back what I find.

Thanks for the report,

On Mon, Jun 8, 2015 at 2:58 AM, Jérémie Knoops <>

> 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
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jun 08 2015 - 05:30:03 PDT
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