[gmx-users] Implemetation of the CHARMM27 ff into gromacs : managment of dihedral terms

Nicolas SAPAY nsapay at ucalgary.ca
Wed Jul 12 00:47:12 CEST 2006

Hello Mark,

Thanks for your scripts. They are well commented and very easy to
understand. Unfornunately, they don't work with my CHARMM parm files. It
is probably a problem of format at the .par begining. I don't know well
Perl but I think I can fix this.

In the conversion made by Yuguang MU, available in the Gromacs site,
improper angles seem to be treated by a periodic function, as said
previously. for exemple, the dihedral angle between O, CT1 NH2 and CC
types is defined as followed in the CHARMM .par
i    j    k    l    Kpsi      ignored   psi0
O    CT1  NH2  CC   45.0000   0         0.0000

after conversion by Yuguang, it becomes in the xxxbon.itp
[ dihedraltypes ]
#define  improper_O_CP1_NH2_CC_  180.00000  94.14000  2

and in the xxx.rtp
[ impropers ]
C NT -CA O improper_O_CP1_NH2_CC_

while in your scripts, impropers are defined in the [ dihedraltypes ] with
function 2. So, I'm not sure to well understand the trick behind that...
May be it depends on the way that CHARMM and Gromacs have implemented
harmonic functions?

Additionally, I have checked how you deal with the 1-4 LJ parameters of
CHARMM.  You define them as comment on the same line than regular LJ
parameters, in the atomtypes section of the xxxnb.itp file, and then
correct them with the second script. It is probably a stupid question (I'm
new in Gromacs :-) ), but is it  a good idea to defined 1-4 parameters in
the [ pairtypes ] section? Let's say that the atom type CT1 is defined
with 1-4 LJ parameters. Then, it can be possible to define all  pair with
CT1 with its 1-4 LJ parameters int the pairtypes section and use them to
produce the .top... It is probably not a bright solution, but if it can


[ Nicolas Sapay Ph.D. ]
University of Calgary, Dept. of Biological Sciences
2500 University Dr. NW, Calgary AB, T2N 1N4, Canada
Tel: (403) 220-6869
Fax: (403) 289-9311

<quote who="Mark Abraham">
>> Hello everybody,
>> I am quite interested by the implementation of the CHARMM27 force field
>> into Gromacs. I have read few messages  on the Gromacs mailing list and
>> have downloaded the CHARMM conversion on this web page:
>> http://www.gromacs.org/old/topologies/force_fields.php
> I also recommend the contribution I made here
> http://www.gromacs.org/contributed_by_users/task,doc_details/gid,59/
>  which I believe to be based on a a more sound conversion technique.
> However the residue topologies, etc. available from the source you cite
> are the only known source of these.
>> So, I have some questions about this translation.
>> - The dihedral terms (proper angles) initially treated by a periodic
>> function have been converted to Ryckeart-Bellemans potential. Why this
>> choice? And how the conversion has been done?
> As described on my above link, and in more detail in my scripts, CHARMM
> sometimes uses two periodic functions for a given dihedral angle with
> different multiplicity. GROMACS does not permit the use of two such
> functions, however. Fortuitously, the combinations of multiplicity and
> phase shift are such that in each case you can use cosine expansions of
> cos (n * phi - delta) = sum_i a_i (cos phi)^i (see standard trigonometry
> works) to express these as a single Ryckaert-Bellemans function. I
> haven't
> verified the other implementation, but my algorithm is clear in the
> scripts I supply and it has been verified against the CHARMM
> implementation of CHARMM27.
>> -  In a same time, improper angles initially treated by harmonic terms
>> have been converted to periodic terms. Why? I'm not sure to understand
>> this choice.
> Sorry, don't recall anything here - can you give an example?
>> Additionally, I have seen that the Urey-Bradley constants were ewritten
>> in
>> the ffcharmmbon.itp file. I guess they are parsed but not really used
>> by
>> Gromacs or the implemtation of the potential has been achieved?
> As you can see in the GROMACS manual, U-B potentials are implemented -
> but
> there was an erroneously-retained fatal warning in versions prior to 3.3
> that you can comment out successfully. The author of the implementation
> of
> CHARMM27 that you cite implemented U-B using normal angle functions plus
> distance restraints, if I recall correctly, which required that you use a
> compatible .mdp file and it was all a bit messy. My scripts use the true
> U-B potentials and again have been verified against the CHARMM
> implementation of CHARMM27.
> Mark
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