[gmx-users] charm in gromacs

[francesco oteri]

Hi,
at the link http://dl.dropbox.com/u/40545409/charmm2itp.tgz you can find
the files I am using

Files ffcharmmnb.itp ffcharmmbon.itp have been generated through:

convert_charmm_to_gromacs.pl par_all36_carb.prm

while carbohydrates.rtp and carbohydrates.rtp through a script of mine.

Now, if you look at [ dihedraltypes ] section in file ffcharmmbon.itp,
there are strange things:

1) dihedrals defined once, are converted Ryckaert-Bellemans form, while the
armonic form should be more clear.
    Anyway, it just a matter of style so I dont complan about.

2) dihedrals with multiple definitions ( OC30P CC3162 CC3161 OC311 at line
598 in file ffcharmmbon.itp, for example) are defined as:
    OC30P CC3162 CC3161 OC311     3 20.92 41.84 16.74 -41.84 0 0
; 30P CC3162 CC3161 OC311     1 180 10.46 1
; 30P CC3162 CC3161 OC311     1 0 8.368 2
; 30P CC3162 CC3161 OC311     1 0 10.46 3

The commented lines clearly display the multiple definition, that can be
described using function 9


3) An other problem rise with impropers dihedrals. Any of them are defined
as Ryckaert-Bellemans,
ex.  HCA1 CC3161 CC3162 OC311     3 0.5858 1.757 0 -2.343 0 0
at line 926 of ffcharmmbon.itp

while   points 1 and 2 don't impact on the correctness of the simulation
and can be bypassed defining
[ bondedtypes ] section as following

1       5          3        2        1           3      1     0

Problem 3 cannot be solved without manipulating the ffcharmmbon.itp.
In fact, since some impropers are defined as functiontype 2 other as
functiontype 3,
so there is not an unique bondedtypes definition covering both the
definition.

Did I any mistake or actually there is a problem in the script?

Francesco




2012/5/18 Mark Abraham <Mark.Abraham at anu.edu.au>

>  On 18/05/2012 2:52 AM, francesco oteri wrote:
>
> Dear gromacs users,
> I am trying to port a set of charm parameter in gromacs.
>
>  I am using the script convert_charmm_to_gromacs.pl contained in the
> file charmm_to_gromacs.tgz (
> http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz).
>
>  Regarding dihedrals, the entry regarding the file says that pdb2gmx
> cannot
>
>  "generate multiple periodic dihedral functions such as CHARMM uses for
> some dihedrals -
> these must be converted to Ryckaert-Bellemans functions, i.e. expressed as
> a cosine power expansion"
>
>  This assumption is no longer valid, is it?
> As far as I know, infact, now gromacs support multiple periodic function
> (funtion 9), is it?
>
>
> Correct, but with the inclusion of native CHARMM27 in GROMACS, I have had
> no reason to upgrade these conversion scripts to support function type 9.
>
> Mark
>
> --
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-- 
Cordiali saluti, Dr.Oteri Francesco
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