Re: amber-developers: Question concerning wildcards in dihedral definitions.

From: Guanglei Cui <>
Date: Tue, 28 Jun 2005 15:14:07 -0700


I just want to add something related to what Ross is seeing here. I
created a topology file for methylmonophosphate with gaff with a
recalculated dihedral profile for dihedral type X -os-p5-X . The
definition in gaff.dat for this term is,

3 2.400(pk) 0.00(phase) 2.0(pn)

First, it's not clear to me why the periodicity is 2 here. I decide to
overwrite the gaff definition with my own parameters (defined in frcmod
as X -os-p5-X ). But what I found in the resulted pmftop (see
attachement), this term was defined twice, one with the gaff term and
another with my parameters. But this didn't seem to affect anything.
This topology file ( gave a good match with the enery
profile calculated with QM, so I assume my definition was used. But it's
confusing though.



Ross Walker wrote:
> Hi All,
> This message concerns some LEaP behaviour that I have found when
> up the message by Angela Liu that was posted to the amber mailing list
> morning. This message was entitled: "AMBER: amber 8 leap topology file
> dihedral term problem"
> I have confirmed the issue in this message and can confirm that Leap
> different numbers of dihedral terms for a copy of a unit. My initial
> conclusions were that the copy command was broken but having dug further
> have found things get considerably more complicated.
> Firstly I have a question concerning how torsion terms involving wild
> should be interpreted. It would be nice to get a definitive answer on
> I.e. In parm99.dat there are the following two terms:
> X -CT-CT-X 9 1.400 0.0 3.
> OS-CT-CT-H1 1 0.250 0.0 1.
> This combination appears for example in a DNA base. Now, in this
> for any dihedrals involving the types OS-CT-CT-H1 what should be written
> the prmtop file? Should it contain just the 0.250 0.0 1. term or
should it
> contain both the 1 fold and the 3 fold term? (0.156 0.0 3.)?
> In other words if a torsion angle is explicitly specified in the parm
> does it override ALL wild card torsion terms that also match or does it
> override ones that have the same periodicity?
> I have always believed it was the former while Dave Case thinks it
should be
> the latter? Can one of the force field developers please let me know
> is correct.
> For the record Leap typically (BUT NOT ALWAYS) seems to employ the
> case, I.e. the 3 fold term is NOT used for the OS-CT-CT-H1 system.
> this seems strange since I would think that one wants to preserve the 3
> rotational barrier for this system... Comments?
> Secondly I just want to ask what the true benefit of wildcards is? Do we
> really need them? Although it would result in a larger parmxx.dat file
> surely it would make things a LOT less ambiguous if we specified every
> dihedral explicitly. The reason I ask this is that leap does not seems
> implement the wild type torsion parameters in a consistent fashion. They
> also cause problems with the copy command in Leap.
> E.g. for a single base of DNA (nuc.pdb attached) if you load that in
> and do the following:
> source leaprc.ff99
> dna = loadpdb nuc.pdb
> dna2 = copy dna
> saveamberparm dna dna.prmtop dna.inpcrd
> saveamberparm dna2 dna2.prmtop dna2.inpcrd
> You will find that dna2.prmtop has 3 extra dihedral terms. These
> to 3 fold X-CT-CT-X being added for O4'-C4'-C5'-H5'1, O4'-C4'-C5'-H5'2
> O4'-C4'-C3'-H3' in addition to the explicitly specified 1 fold
> term. However, other examples where this X-CT-CT-X term should be added
> things were consistent would be H4'-C4'-C3'-O3' (there are many other
> examples as well). In both the original AND the copy only the 1 fold
> (0.250 0.00 1.0) is present. Strangely if you do:
> dna3 = copy dna2
> saveamberparm dna3 dna3.prmtop dna3.inpcrd
> you get back to dna.prmtop.
> So in this case, the file dna.prmtop is correct assuming that ANY
> specified torsion parameter should overide the wild card parameters even
> the phase does not match. While dna2.prmtop is definately wrong as it
> has SOME of the wild card matches added.
> However, the story does not end here. If you load nma.pdb (attached) and
> nma = loadpdb nma.pdb
> nma2 = copy nma
> saveamberparm nma nma.prmtop nma.inpcrd
> saveamberparm nma2 nma2.prmtop nma2.inpcrd
> You will find that in this case the nma.prmtop has MORE dihedral terms
> the nma2.prmtop. Although this time the two prmtop files give the same
> energies since the extra dihedral terms have zero barrier height.
> this is fortuitous in my opinion and indicative of a deeper problem. If
> print out the dihedrals with rdparm you'll see that the first prmtop has
> following two extra terms:
> 10: 0.000 0.00 2.00 :1.HH32 :1.CH3 :1.C :1.O (3,2,5,6)
> 15: 0.000 0.00 2.00 :1.HH31 :1.CH3 :1.C :1.O (1,2,5,6)
> Two things are very strange here. Firstly there is are two explicit
> HC-CT-C-O dihedrals:
> HC-CT-C-O 1 0.80 0.0 -1.
> HC-CT-C-O 1 0.08 180.0 3.
> Both of which are included. Now, if leap was being consistent in it's
> treatment of wild type parameters as in the DNA case above then that
> be all there is in the prmtop file. In the one created from the COPIED
> this is true but in the uncopied one, the one created by loading the pdb
> file leap has included the X-C -CT- X 2 fold term. BUT it has only
> it for 2 out of the 3 hydrogens!!! Why??? Fortunately here it doesn't
> any difference since the barrier height is zero but if you were to make
> X-C -CT- X term non-zero you would have a serious problem.
> These are just two simple examples, I'm sure there are many more and
> serious examples.
> I think we should check very carefully that the parameters to which the
> force fields are being fit are the same as those generated for the
> file. Should we perhaps do away with the wild cards all together to
> these ambiguities???
> Your comments....
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
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Received on Wed Apr 05 2006 - 23:49:55 PDT
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