[gmx-users] charm in gromacs
francesco.oteri at gmail.com
Fri May 18 12:02:32 CEST 2012
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:
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
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
so there is not an unique bondedtypes definition covering both the
Did I any mistake or actually there is a problem in the script?
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 (
> Regarding dihedrals, the entry regarding the file says that pdb2gmx
> "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 This assumption is no longer valid, is it?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.
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Cordiali saluti, Dr.Oteri Francesco
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